Modulation of replicative fitness by deoptimization of synonymous codons

ABSTRACT

Methods of producing a pathogen with reduced replicative fitness are disclosed, as are attenuated pathogens produced using the methods. In particular examples, the method includes deoptimizing one or more codons in a coding sequence, thereby reducing the replicative fitness of the pathogen. Methods of using the attenuated pathogens as immunogenic compositions are also disclosed.

CROSS REFERENCE TO RELATED APPLICATIONS

This is a divisional of co-pending U.S. application Ser. No. 14/464,619,filed Aug. 20, 2014, which is a divisional of U.S. application Ser. No.11/576,941, filed Nov. 19, 2007, now U.S. Pat. No. 8,846,051, issuedSep. 30, 2014, which is the U.S. National Stage of InternationalApplication No. PCT/US2005/036241, filed Oct. 7, 2005, which waspublished in English under PCT Article 21(2), which in turn claimsbenefit of U.S. Provisional Application No. 60/617,545 filed Oct. 8,2004. Each application is incorporated by reference in its entirety.

ACKNOWLEDGMENT OF GOVERNMENT SUPPORT

This invention was made by the National Center for Infectious Diseases,Centers for Disease Control and Prevention, an agency of the UnitedStates Government. Therefore, the U.S. Government has certain rights inthis invention.

FIELD

This disclosure relates to methods of reducing the replicative fitnessof a pathogen by deoptimizing codons. Pathogens with deoptimized codonscan be used to increase the phenotypic stability of attenuated vaccines.

BACKGROUND

Infections by intracellular pathogens such as viruses, bacteria andparasites, are cleared in most cases after activation of specific Tcellular immune responses that recognize foreign antigens and eliminateinfected cells. Vaccines against those infectious organisms have beentraditionally developed by administration of whole live attenuated orinactivated microorganisms. Although research has been performed usingsubunit vaccines, the levels of cellular immunity induced are usuallylow and not capable of eliciting complete protection against diseasescaused by intracellular microbes.

One problem encountered when using live attenuated vaccines is thedevelopment of adverse events in some patients. Typical reactionsassociated with live viral and bacterial vaccines, such as measles,mumps, rubella (MMR) and varicella vaccines, often resemble attenuatedforms of the disease against which the vaccine is directed. However,more severe adverse affects have been reported. For example, there is anassociation between the Urabe strain of mumps vaccine and viralmeningitis (Dubey and Banerjee, Indian J. Pediatr. 70:579-84, 2003). Inaddition, vaccine associated thrombocytopenia has been reported.Although epidemiological studies do not support a causative link betweenMMR and autism (Chen et al., Psychol. Med. 34:543-53, 2004), the fearremains and likely contributes to poor vaccine acceptance in someregions and sections of society.

In addition, documented safety concerns with vaccines demonstrate theharm that vaccines can cause. For example, the currently availableattenuated Sabin oral polio vaccine (OPV) strains are geneticallyunstable, principally because only 2-5 base substitutions confer theattenuated phenotype (Ren et al. J. Virol. 65:1377-82, 1991). Thisinstability is the underlying cause of vaccine-associated paralyticpoliomyelitis in immunologically normal (Strebel et al., Clin. Infect.Dis. 14:568-79, 1992) and in people with B-cell immunodeficiencies (Kewet al., J. Clin. Microbiol. 36:2893-9; Khetsuriani et al., J. Infect.Dis 188:1845-52, 2003; Yang et al., J. Virol. 79:12623-34), and ofoutbreaks associated with circulating vaccine-derived polioviruses (Kewet al., Science 296: 356-9, 2002; Yang et al., J. Virol. 77:8366-77,2003; Rousset et al., Emerg. Inf. Dis. 9:885-7, 2003; Kew et al., Bull.WHO 82:16-23, 2004; Shimizu et al., J. Virol. 78:13512-21, 2004; Kew etal., Ann. Rev. Microbiol. 59:587-635, 2005). In addition, the CDCrecommended suspending use of the rhesus-human rotavirusreassortant-tetravalent vaccine (RRV-TV) due to cases of intussusception(a bowel obstruction in which one segment of bowel becomes enfoldedwithin another segment) among infants who received the vaccine (MMWRMorb Mortal Wkly Rep. 53:786-9, 2004).

Although the primary mode of protective immunity induced by OPV is theproduction of neutralizing antibody by B-cells, OPV stimulates an immuneresponse similar to that of a natural infection. Immunity againstparalytic disease is further enhanced by the production of antibodies inthe gastrointestinal tract that limit poliovirus replication, and, thus,person-to-person transmission. The stimulation of intestinal immunity,along with ease of administration, has made OPV the vaccine of choicefor global polio eradication (Aylward and Cochi, Bull. WHO 82:40-6,2004). Therefore, there is a need to identify methods of making anattenuated vaccine that reduces the safety concerns with currentlyavailable live attenuated vaccines while retaining the advantages ofattenuated vaccines.

SUMMARY

The inventors have determined that replacement of one or more natural(or native) codons in a pathogen with synonymous unpreferred codons candecrease the replicative fitness of the pathogen, thereby attenuatingthe pathogen. The unpreferred synonymous codon(s) encode the same aminoacid as the native codon(s), but have nonetheless been found to reduce apathogen's replicative fitness. The introduction of deoptimized codonsinto a pathogen can limit the ability of the pathogen to mutate or touse recombination to become virulent. The disclosed compositions andmethods can be used in attenuated vaccines having well-defined levels ofreplicative fitness and enhanced genetic stabilities.

Methods of reducing a pathogen's replicative fitness are disclosed. Insome examples, the method includes deoptimizing at least one codon in acoding sequence of the pathogen, thereby generating a deoptimized codingsequence. Such deoptimization reduces replicative fitness of thepathogen. In some examples, more than one coding sequence of thepathogen is deoptimized, such as at least one, at least two, or at least5 coding sequences, such as deoptimizing 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10coding sequences of the pathogen.

More than one codon in the one or more coding sequences can bedeoptimized, such as at least 15 codons, at least 20 codons, at least 30codons, at least 40 codons, at least 50 codons, at least 60 codons, atleast 70 codons, at least 100 codons, at least 200 codons, at least 500codons, or even at least 1000 codons, in each coding sequence. In someexamples, at least 20% of the coding sequence of each desired gene isdeoptimized, such as at least 30%, at least 40%, at least 50%, at least60%, at least 70%, at least 80%, at least 90%, at least 95%, or even atleast 97% deoptimized.

In particular examples, deoptimizing the codon composition alters theG+C content of a coding sequence, such as increases or decreases the G+Ccontent by at least 10%, for example increases the G+C content of acoding sequence by at least 10%, such as at least 20%, at least 30%, atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, oreven by at least 90%, or decreases the G+C content of a coding sequenceby at least 10%, such as at least 20%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 80%, or even by at least90%. However, the G+C content can be altered in combination withdeoptimizing one or more codons in a pathogen sequence. For example,some of the nucleotide substitutions can be made to deoptimize codons(which may or may not alter the G+C content of the sequence), and othernucleotide substitutions can be made to alter the G+C content of thesequence (which may or may result in a deoptimized codon). Altering theG+C content of the sequence may also result in a deoptimized codon, butis not required in all instances.

For example, if the pathogen is a rubella virus, whose RNA genome has ahigh G+C content and consequently has a high rate of usage of rarecodons rich in G+C. Therefore, deoptimization of rubella virus can beachieved by decreasing the G+C content of one or more coding sequences,for example decreasing the G+C content by at least 10%, such as at least20%, or even by at least 50%. In another example, the pathogen is apoliovirus, and deoptimization can be achieved by increasing the G+Ccontent of one or more coding sequences, for example increasing the G+Ccontent by at least 10%, such as at least 20%, or even by at least 50%.

In some examples, deoptimizing the codon composition alters thefrequency of CG dinucleotides, TA dinucleotides, or both, in a codingsequence, such as increases or decreases the frequency of CG or TAdinucleotides by at least 10%, for example increases in the number of CGor TA dinucleotides in a coding sequence by at least 10%, such as atleast 20%, at least 30%, at least 40%, at least 50%, at least 60%, atleast 100%, at least 200%, or even by at least 300%, or decreases in thenumber of CG or TA dinucleotides in a coding sequence by at least 10%,such as at least 20%, at least 30%, at least 40%, at least 50%, at least60%, at least 70%, at least 80%, or even by at least 90%. However, thenumber of CG or TA dinucleotides can be altered in combination withdeoptimizing one or more codons in a pathogen sequence. For example,some of the nucleotide substitutions can be made to deoptimize codons(which may or may not alter the number of CG or TA dinucleotides in thesequence), and other nucleotide substitutions can be made to alter thenumber of CG or TA dinucleotides in the coding sequence (which may ormay result in a deoptimized codon). Altering the number of CG or TAdinucleotides in the sequence may also result in a deoptimized codon,but is not required in all instances.

For example, if the pathogen is a poliovirus or eukaryotic virus,deoptimization can be achieved by increasing the number of CG or TAdinucleotides in one or more coding sequences, for example increasingthe number of CG or TA dinucleotides by at least 10%, such as at least30%, or even by at least 300%. In another example, the pathogen is abacterium, and deoptimization can be achieved by decreasing the numberof CG or TA dinucleotides in one or more coding sequences, for exampledecreasing the number of CG or TA dinucleotides by at least 10%, such asat least 30%, or even by at least 50%.

In particular examples, methods of reducing the replicative fitness of apathogen include analysis of a codon usage table for the pathogen toidentify amino acids that are encoded by at least 2 different codons,(such as 2 different codons, 3 different codons, 4 different codons, or6 different codons), and choosing the codon used least frequently(lowest codon usage frequency) of the different codons in the pathogen.The one or more low-frequency codons chosen are used to replace theappropriate one or more codons in the native sequence, for example usingmolecular biology methods, thereby generating a deoptimized sequencethat reduces the replicative fitness of the pathogen. For example, ifthe pathogen uses the CCU, CCC, CCA and CCG codons to encode for Pro at12, 19, 21 and 9% frequency respectively, the CCG codon can be used toreplace at least one CCU, CCC, or CCA codon in the native pathogensequence, thereby generating a deoptimized sequence. In this example,the use of the CCG codon may also increase the number of CGdinucleotides in the sequence, and may also increase the G+C content ofthe sequence. In examples where the amino acid is encoded by only twodifferent codons, one of the two codons can be selected and used in thedeoptimized sequence if the codon usage is highly biased, such as adifference of at least 10%, at least 20%, or at least 30%. For example,if the pathogen uses the codons CAA and CAG to encode for Gln at 60% and40% frequency respectively, the CAG codon is used to replace at leastone CAA codon in the native sequence, thereby generating a deoptimizedsequence. In this example, the use of the CAG codon may also increasethe G+C content of the sequence.

In some examples, when choosing a low frequency codon, the codon chosenbased on its ability to alter the G+C content of the deoptimizedsequence or alter the frequency of CG or TA dinucleotides. For example,if the pathogen uses the CCU, CCC, CCA and CCG codons to encode for Proat 9, 19, 21 and 12% frequency respectively, the CCG codon can be usedto replace at least one CCU, CCC, or CCA codon in the native pathogensequence, if the presence of increased G+C content or increased numbersof CG dinucleotides is desired in the deoptimized sequence. Even thoughCCG is not the most infrequently used codon, the use of this codon willincrease the number of CG dinucleotides in the sequence and may increasethe G+C content of the deoptimized sequence. In contrast, if thepresence of decreased G+C content or decreased numbers of CGdinucleotides is desired in the deoptimized sequence, the CCU codoncould be used to replace at least one CCG, CCC, or CCA codon in thenative pathogen sequence.

In some examples, there may be two or more codons used at lowfrequencies that are similar in value, such as codon usages that arewithin 0.01-2% of each other (for example within 0.1-2%, 0.5-2% or 1-2%of each other). In this case, one can opt to not choose the codon withthe lowest codon usage frequency. In some examples, the codon chosen isone that will alter the G+C content of the deoptimized sequence, such asincrease or decrease the G+C content of the sequence. In other examples,the codon chosen is one that increases or decreases the frequency of aspecific dinucleotide pair (such as a CG or TA dinucleotide pair) foundat low frequencies in that genome (such as no more than 4%, for exampleno more than 3%). Such dinucleotide pairs can fall across codonboundaries, or be contained within the codon.

The codon usage table used can include codon usage data from thecomplete genome of the pathogen (or 2 or more genomes, for example fromdifferent strains of the pathogen), codon usage data from one or moregenes (such as 1 gene, at least 2 genes, at least 3 genes, at least 5genes, or even at least 10 genes), for example one or more genesinvolved in the antigenicity of the pathogen.

Specific non-limiting examples of deoptimized coding sequences forseveral pathogens are disclosed herein. In some examples, a deoptimizedcoding sequence includes a nucleic acid sequence having at least 90%sequence identity, such as at least 95% sequence identity, to any of SEQID NOS: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51,54, 55, 56, 57, 58, 67, 68, or 69. Sequences that hybridize to any ofSEQ ID NOS: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48,51, 54, 55, 56, 57, 58, 67, 68, or 69, for example under stringentconditions, are also disclosed. In some examples, a deoptimized codingsequence includes a nucleic acid sequence shown in any of SEQ ID NOS: 5,8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 55, 56,57, 58, 67, 68, or 69.

In particular examples, more than one coding sequence in the pathogen isdeoptimized, such as at least 2 coding sequences, such as at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, oreven at least 10 coding sequences. Any coding sequence can bedeoptimized. In one example, one of the deoptimized coding sequencesencodes for a housekeeping gene. Particular examples of coding sequencesthat can be deoptimized in a pathogen, include, but are not limited to,sequences that encode a viral capsid, a viral spike glycoprotein (forexample the gH and gE surface glycoproteins of varicella-zoster virus);glycoprotein B, glycoprotein D, glycoprotein H, and glycoprotein N ofhuman cytomegalovirus; glycoprotein D, tegument protein host shut-offfactor, ribonucleotide reductase large subunit of human herpes simplexviruses; the fusion (F) protein and glycoprotein (G) of respiratorysyncytial virus; the hemagglutinin (HA) and neuraminidase (NA)glycoproteins of influenza virus; the env protein of humanimmunodeficiency virus type 1 (HIV-1), ArgS and TufA gene products ofEscherichia coli, or combinations thereof.

The replicative fitness of the pathogen can be reduced by any amountsufficient to attenuate the pathogen. In some examples, the replicativefitness of the deoptimized pathogen is reduced by at least 20%, such asat least 30%, at least 40%, at least 48%, at least 50%, at least 75%, atleast 80%, at least 90%, at least 95%, or even at least 97%, as comparedto replicative fitness of a pathogen (of the same species and strain)having a coding sequence with an optimized codon composition.

Any pathogen can be attenuated using the disclosed methods. Particularexamples include, but are not limited to, viruses (such aspositive-strand RNA viruses, negative-strand RNA viruses, DNA viruses,and retroviruses), bacteria, fungi, and protozoa.

In one specific example, the pathogen is a poliovirus. For example, whenthe natural codons of the Sabin type 2 (Sabin 2) OPV strain (Sabin andBoulger. J. Biol. Stand. 1:115-8; 1973; Toyoda et al., J. Mol. Biol.174:561-85, 1984) were replaced with synonymous unpreferred codons insequences encoding capsid proteins, virus plaque size and yield in cellculture decreased in proportion to the number of unpreferred codonsincorporated into the capsid sequences. The altered codon compositionwas largely conserved during 25 serial passages in HeLa cells. Fitnessfor replication in HeLa cells of both the unmodified Sabin 2 andmodified constructs increased with higher passage; however, the relativefitness of the modified constructs remained lower than that of theunmodified construct.

Attenuated pathogens produced by the methods disclosed herein are alsoprovided. In one example, immunogenic compositions include an attenuatedpathogen produced by the disclosed methods. Such immunogeniccompositions can include other agents, such as an adjuvant, apharmaceutically acceptable carrier, or combinations thereof.

Methods are disclosed for eliciting an immune response against apathogen in a subject, using the disclosed attenuated pathogens. In oneexample, the method includes administering an immunologically effectiveamount of the disclosed attenuated pathogens to a subject, therebyeliciting an immune response in the subject. In particular examples, thedisclosed attenuated pathogens are present in an immunogenic compositionwhich is administered to a subject. Subjects include human andveterinary subjects, such as cats, dogs, cattle, sheep, pigs and horses.

The foregoing and other features and advantages of the disclosure willbecome more apparent from the following detailed description of aseveral embodiments.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is a schematic drawing showing the locations of the codonreplacement cassettes A-D in the infectious Sabin 2 (S2R9) cDNA clone.The restriction sites used for construction of the codon replacementconstructs are indicated at the appropriate positions, in the context ofthe mature viral proteins.

FIGS. 1B-1D is a sequence showing original S2R9 Sabin 2 triplets (ABCD,SEQ ID NO: 3) above the codon-replacement residues; the deduced aminoacids for both constructs are indicated below the triplets (SEQ ID NO:4). The fully replaced sequence (abcd, SEQ ID NO: 5) is referred toS2R23.

FIG. 2 is a schematic drawing showing exemplary Sabin 2 codonreplacement constructs. The Sabin 2 genome is represented with openrectangles. Filled rectangles indicate the locations of individualcassettes, black-filled rectangles indicate cassettes with replacementcodons. Unmodified cassettes are indicated by upper case letters; thecorresponding cassettes with replacement codons are indicated by lowercase letters.

FIG. 3A is a graph showing mean plaque area in HeLa cells versus thenumber of nucleotide substitutions in the capsid region. The coefficientof determination (R²) for the regression line was 0.88.

FIG. 3B is a graph showing virus yields (12-hour postinfection) of asingle-step growth curve versus the number of nucleotide substitutionsin the capsid region. The coefficient of determination (R²) for theregression line was 0.94.

FIG. 3C is a digital image showing plaque phenotypes at 35° C. in HeLacells.

FIG. 3D is a graph showing the inverse linear relationship observedbetween plaque area and number of replacement codons in Sabin 2.

FIG. 3E is a graph showing the inverse linear relationship observedbetween plaque area and number of CG pairs in Sabin 2.

FIGS. 4A and 4B are graphs showing single-step growth curves in HeLa S3cells at 35° C.

FIGS. 5A and 5B are digital images showing production of intracellularPoliovirus-specific proteins produced by ABCD, ABCd, and abcd viruses invivo and in vitro. (A) Lysates of infected HeLa cells labeled with[³⁵S]methionine at 4 to 7 hours postinfection. (B) In vitro translationproducts from rabbit reticulocyte lysates programmed with 250 ng of RNAtranscripts from cDNAs ABCD, ABCd, and abcd. Noncapsid proteins wereidentified by their electrophoretic mobilities and band intensities;capsid proteins were identified by their comigration with proteins frompurified virions.

FIGS. 5C and 5D are digital images showing production of intracellularMEF Poliovirus-specific proteins produced by ABC, ABc, and abc virusesin vivo and in vitro. (A) Lysates of infected HeLa cells labeled with[³⁵S]methionine at 4 to 7 hours postinfection. (B) In vitro translationproducts from rabbit reticulocyte lysates programmed with 250 ng of RNAtranscripts from cDNAs ABC, ABc, and abc. Noncapsid proteins wereidentified by their electrophoretic mobilities and band intensities;capsid proteins were identified by their comigration with proteins frompurified virions.

FIGS. 6A and 6B are graphs showing RNA yields from (A) ABCD, ABCd, andabcd Sabin 2 viruses obtained in the single-step growth experimentsdescribed in FIGS. 4A and 4B, and for (B) ABC, ABc, and abc MEF1viruses. RNA levels were determined by quantitative PCR using primersand a probe targeting 3D^(pol) region sequences. One pg of poliovirusRNA corresponds to ˜250,000 genomes.

FIG. 7 shows MinE RNA secondary structures for complete genomes of ABCD,ABCd, and abcd viruses calculated by using the mfold algorithm. Basepositions are numbered in increments of 1000. Triangles mark boundariesof codon-replacement cassettes: beginning of cassette A (nt 657);beginning of cassette D (nt 2616); end of cassette D (nt 3302). Onlyintervals bounded by filled triangles had replacement codons.

FIG. 8A is a graph showing mean plaque areas of evolving viruses using aplaque assay of HeLa cells after 60 hours incubation at 35° C.

FIG. 8B is a graph showing virus titers determined by plaque assay ofHeLa cells at 35° C. on every fifth passage.

FIG. 8C is a digital image showing plaque phenotypes at 35° C. in HeLacells (35° C., 60 hours).

FIGS. 9A-E show an original MEF1 capsid sequence (SEQ ID NO: 6; GenBankAccession No. AY082677) above the codon-replacement residues for an MEF1de-optimized capsid sequence (SEQ ID NO: 8) (only replaced nucleotidesare indicated); the deduced amino acids for both the constructs areindicated below the triplets (SEQ ID NO: 7).

FIG. 9F is a graph showing the inverse linear relationship observedbetween plaque area and number of replacement codons in MEF1.

FIG. 9G is a graph showing the inverse linear relationship observedbetween plaque area and number of CG pairs in MEF1.

FIG. 9H is a graph showing plaque yields over time for native anddeoptimized MEF1 constructs.

FIG. 9I is a graph showing the inverse linear relationship observedbetween plaque size and number of nucleotide changes in MEF1.

FIG. 9J is a graph showing the inverse linear relationship observedbetween viral titer and number of nucleotide changes in MEF1.

FIGS. 10A-10B show an original FMDV capsid sequence (SEQ ID NO: 9;GenBank Accession No. AJ539141) above the codon-replacement residues foran FMDV de-optimized capsid sequence (SEQ ID NO: 11) (only replacednucleotides are indicated); the deduced amino acids are indicated belowthe triplets (SEQ ID NO: 10).

FIGS. 11A-11C show an original SARS spike glycoprotein sequence (SEQ IDNO: 12; GenBank Accession No. AY278741) above the codon-replacementresidues for a de-optimized SARS spike glycoprotein sequence (SEQ ID NO:14) (only replaced nucleotides are indicated); the deduced amino acidsare indicated below the triplets (SEQ ID NO: 13).

FIGS. 12A-12G shows an original rubella sequence (SEQ ID NO: 15; GenBankAccession No. L78917) above the codon-replacement residues for ade-optimized rubella sequence (SEQ ID NO: 18) (only replaced nucleotidesare indicated); the deduced amino acids are indicated below the triplets(SEQ ID NOS: 16 and 17).

FIGS. 13A-B show an original VZV gH sequence (GenBank Accession No.AB097932, SEQ ID NO: 19) above the codon-replacement residues for ade-optimized VZV gH sequence (SEQ ID NO: 21) (only replaced nucleotidesare indicated); the deduced amino acids are indicated below the triplets(SEQ ID NO: 20).

FIGS. 14A-B show an original VZV gE sequence (GenBank Accession No.AB097933, SEQ ID NO: 22) above the codon-replacement residues for ade-optimized VZV gE sequence (SEQ ID NO: 24) (only replaced nucleotidesare indicated); the deduced amino acids are indicated below the triplets(SEQ ID NO: 23).

FIGS. 15A-B show an original measles F sequence (SEQ ID NO: 25; GenBankAccession No. AF266287) above the codon-replacement residues for ade-optimized measles F sequence (SEQ ID NO: 27) (only replacednucleotides are indicated); the deduced amino acids are indicated belowthe triplets (SEQ ID NO: 26).

FIGS. 16A-B show an original measles hemagglutinin (H) sequence (SEQ IDNO: 28; GenBank Accession No. AF266287) above the codon-replacementresidues for a de-optimized measles H sequence (SEQ ID NO: 30) (onlyreplaced nucleotides are indicated); the deduced amino acids areindicated below the triplets (SEQ ID NO: 29).

FIGS. 17A-B show an original RSV F sequence (SEQ ID NO: 31; GenBankAccession No. U63644) above the codon-replacement residues for ade-optimized RSV F sequence (SEQ ID NO: 33) (only replaced nucleotidesare indicated); the deduced amino acids are indicated below the triplets(SEQ ID NO: 32).

FIG. 18 shows an original RSV G sequence (SEQ ID NO: 34; GenBankAccession No. U63644) above the codon-replacement residues for ade-optimized RSV G sequence (SEQ ID NO: 36) (only replaced nucleotidesare indicated); the deduced amino acids are indicated below the triplets(SEQ ID NO: 35).

FIG. 19 shows an original influenza HA sequence (SEQ ID NO: 37) abovethe codon-replacement residues for a de-optimized influenza HA sequence(SEQ ID NO: 39) (only replaced nucleotides are indicated); the deducedamino acids are indicated below the triplets (SEQ ID NO: 38).

FIG. 20 shows an original influenza NA sequence (SEQ ID NO: 40) abovethe codon-replacement residues for a de-optimized influenza NA sequence(SEQ ID NO: 42) (only replaced nucleotides are indicated); the deducedamino acids are indicated below the triplets (SEQ ID NO: 41).

FIGS. 21A-21B show an original HIV-1 env sequence (SEQ ID NO: 43;GenBank Accession No. AF110967) above the codon-replacement residues fora de-optimized HIV-1 env sequence (SEQ ID NO: 45) (only replacednucleotides are indicated); the deduced amino acids are indicated belowthe triplets (SEQ ID NO: 44).

FIGS. 22A-22B show an original E. coli ArgS sequence (SEQ ID NO: 46;GenBank Accession No. U0096) above the codon-replacement residues for ade-optimized E. coli ArgS sequence (SEQ ID NO: 48) (only replacednucleotides are indicated); the deduced amino acids are indicated belowthe triplets (SEQ ID NO: 47).

FIG. 23 shows an original E. coli TufA sequence (SEQ ID NO: 49; GenBankAccession No. J01690) above the codon-replacement residues for ade-optimized E. coli TufA sequence (SEQ ID NO: 51) (only replacednucleotides are indicated); the deduced amino acids are indicated belowthe triplets (SEQ ID NO: 50).

FIGS. 24A-24M show exemplary codon usage tables for various pathogens.

FIG. 25 shows a Sabin 2 virus cassette d (VP1 region) sequence that hasbeen altered by reducing the number of CG dinucleotides. The originalsequence (nucleotides 1975-2664 of SEQ ID NO: 3) is shown above thecodon-replacement residues for an altered Sabin 2 cassette d (VP1region) sequence (SEQ ID NO: 65) (only replaced nucleotides areindicated); the deduced amino acids are indicated below the triplets(amino acids 623-852 of SEQ ID NO: 4).

FIG. 26 shows a Sabin 2 virus cassette d (VP1 region) sequence that hasbeen altered by decreasing the number of CG and TA dinucleotides. Theoriginal sequence (nucleotides 1975-2664 of SEQ ID NO: 3) is shown abovethe codon-replacement residues for an altered Sabin 2 cassette d (VP1region) sequence (SEQ ID NO: 66) (only replaced nucleotides areindicated); the deduced amino acids are indicated below the triplets(amino acids 623-852 of SEQ ID NO: 4).

FIG. 27 shows a Sabin 2 virus cassette d (VP1 region) sequence that hasbeen altered by increasing the number of CG dinucleotides. The originalsequence (nucleotides 1975-2664 of SEQ ID NO: 3) is shown above thecodon-replacement residues for a de-optimized Sabin 2 cassette d (VP1region) sequence (SEQ ID NO: 67) (only replaced nucleotides areindicated); the deduced amino acids are indicated below the triplets(amino acids 623-852 of SEQ ID NO: 4). Original CG dinucleotidesretained after codon changes are underlined.

FIG. 28 shows a Sabin 2 virus cassette d (VP1 region) sequence that hasbeen altered by increasing the number of CG and TA dinucleotides. Theoriginal sequence (nucleotides 1975-2664 of SEQ ID NO: 3) is shown abovethe codon-replacement residues for a de-optimized Sabin 2 cassette d(VP1 region) sequence (SEQ ID NO: 68) (only replaced nucleotides areindicated); the deduced amino acids are indicated below the triplets(amino acids 623-852 of SEQ ID NO: 4). Original CG, TA dinucleotidesretained after codon changes are underlined.

FIG. 29 shows a Sabin 2 virus cassette d (VP1 region) sequence havingmaximum codon deoptimization. The original sequence (nucleotides1975-2664 of SEQ ID NO: 3) is shown above the codon-replacement residuesfor the de-optimized Sabin 2 cassette d (VP1 region) sequence (SEQ IDNO: 69) (only replaced nucleotides are indicated); the deduced aminoacids are indicated below the triplets (amino acids 623-852 of SEQ IDNO: 4). Original CG dinucleotides retained after codon changes areunderlined.

FIG. 30 shows a Sabin 2 virus cassette d (VP1 region) sequence that hasMEF1 codons for Sabin 2 amino acids. The original sequence (nucleotides1975-2664 of SEQ ID NO: 3) is shown above the codon-replacementresidues; the deduced amino acids are indicated below the triplets(amino acids 623-852 of SEQ ID NO: 4). The altered Sabin 2 cassette d(VP1 region) sequence (SEQ ID NO: 70) is shown below the originalsequence (only replaced nucleotides are indicated). The amino acids thatdiffer between Sabin 2 and MEF-1 are underlined.

SEQUENCE LISTING

The nucleic acid and amino acid sequences listed in the accompanyingsequence listing are shown using standard letter abbreviations fornucleotide bases, and three-letter code for amino acids. Only one strandof each nucleic acid sequence is shown, but the complementary strand isunderstood as included by any reference to the displayed strand. TheSequence Listing is submitted as an ASCII text file in the form of thefile named Sequence_Listing.txt, which was created on Aug. 22, 2017, andis 485,926 bytes, which is incorporated by reference herein.

SEQ ID NO: 1 is a primer sequence used to reverse transcribe polioviruscDNA.

SEQ ID NO: 2 is a primer sequence used to long PCR amplify polioviruscDNA.

SEQ ID NO: 3 is a capsid nucleic acid coding sequence of Sabin 2(construct S2R9) poliovirus.

SEQ ID NO: 4 is a protein sequence encoded by SEQ ID NO: 3.

SEQ ID NO: 5 is a Sabin 2 codon-deoptimized nucleic acid sequence.

SEQ ID NO: 6 is a capsid nucleic acid coding sequence of MEF1poliovirus.

SEQ ID NO: 7 is a protein sequence encoded by SEQ ID NO: 6.

SEQ ID NO: 8 is an MEF1 codon-deoptimized nucleic acid sequence.

SEQ ID NO: 9 is a capsid nucleic acid coding sequence of FMDV.

SEQ ID NO: 10 is a protein sequence encoded by SEQ ID NO: 9.

SEQ ID NO: 11 is an FMDV codon-deoptimized capsid nucleic acid sequence.

SEQ ID NO: 12 is a spike glycoprotein nucleic acid coding sequence ofSARS coronavirus.

SEQ ID NO: 13 is a protein sequence encoded by SEQ ID NO: 12.

SEQ ID NO: 14 is a SARS coronavirus codon-deoptimized spike glycoproteinnucleic acid sequence.

SEQ ID NO: 15 is a nucleic acid coding sequence of rubella virus.

SEQ ID NOS: 16 and 17 are protein sequences encoded by SEQ ID NO: 15.

SEQ ID NO: 18 is a rubella codon-deoptimized nucleic acid sequence.

SEQ ID NO: 19 is a gH nucleic acid coding sequence of VZV.

SEQ ID NO: 20 is a protein sequence encoded by SEQ ID NO: 18.

SEQ ID NO: 21 is a VZV codon-deoptimized gH nucleic acid sequence.

SEQ ID NO: 22 is a gE nucleic acid coding sequence of VZV.

SEQ ID NO: 23 is a protein sequence encoded by SEQ ID NO: 21.

SEQ ID NO: 24 is a VZV codon-deoptimized gE nucleic acid sequence.

SEQ ID NO: 25 is an F nucleic acid coding sequence of measles virus.

SEQ ID NO: 26 is a protein sequence encoded by SEQ ID NO: 24.

SEQ ID NO: 27 is a measles virus codon-deoptimized F nucleic acidsequence.

SEQ ID NO: 28 is a hemagglutinin (H) nucleic acid coding sequence ofmeasles virus.

SEQ ID NO: 29 is a protein sequence encoded by SEQ ID NO: 27.

SEQ ID NO: 30 is a measles codon-deoptimized H nucleic acid sequence.

SEQ ID NO: 31 is an F nucleic acid coding sequence of RSV.

SEQ ID NO: 32 is a protein sequence encoded by SEQ ID NO: 30.

SEQ ID NO: 33 is a RSV codon-deoptimized F nucleic acid sequence.

SEQ ID NO: 34 is a G nucleic acid coding sequence of RSV.

SEQ ID NO: 35 is a protein sequence encoded by SEQ ID NO: 33.

SEQ ID NO: 36 is a RSV codon-deoptimized G nucleic acid sequence.

SEQ ID NO: 37 is a HA nucleic acid coding sequence of influenza virus.

SEQ ID NO: 38 is a protein sequence encoded by SEQ ID NO: 36.

SEQ ID NO: 39 is an influenza virus codon-deoptimized HA nucleic acidsequence.

SEQ ID NO: 40 is a NA nucleic acid coding sequence of influenza virus.

SEQ ID NO: 41 is a protein sequence encoded by SEQ ID NO: 39.

SEQ ID NO: 42 is an influenza codon-deoptimized NA nucleic acidsequence.

SEQ ID NO: 43 is an env nucleic acid coding sequence of HIV-1.

SEQ ID NO: 44 is a protein sequence encoded by SEQ ID NO: 42.

SEQ ID NO: 45 is an HIV-1 codon-deoptimized env nucleic acid sequence.

SEQ ID NO: 46 is an ArgS nucleic acid coding sequence of E. coli.

SEQ ID NO: 47 is a protein sequence encoded by SEQ ID NO: 45.

SEQ ID NO: 48 is an E. coli codon-deoptimized ArgS nucleic acidsequence.

SEQ ID NO: 49 is an TufA nucleic acid coding sequence of E. coli.

SEQ ID NO: 50 is a protein sequence encoded by SEQ ID NO: 48.

SEQ ID NO: 51 is an E. coli codon-deoptimized TufA nucleic acidsequence.

SEQ ID NO: 52 is a nucleic acid sequence showing the sequence of MEF1R1or uncloned.

SEQ ID NO: 53 is a nucleic acid sequence showing the sequence of MEF1R2.

SEQ ID NO: 54 is a nucleic acid sequence showing the sequence of MEF1R5.

SEQ ID NO: 55 is a nucleic acid sequence showing the sequence of MEF1R6.

SEQ ID NO: 56 is a nucleic acid sequence showing the sequence of MEF1R7.

SEQ ID NO: 57 is a nucleic acid sequence showing the sequence of MEF1R8.

SEQ ID NO: 58 is a nucleic acid sequence showing the sequence of MEF1R9.

SEQ ID NOS: 59-60 are primer sequences used to amplify the 3D^(pol)region of Sabin 2.

SEQ ID NO: 61 is a TaqMan probe used to detect the yield of amplicongenerated using SEQ ID NOS: 59 and 60.

SEQ ID NOS: 62-63 are primer sequences used to amplify the 3D^(pol)region of MEF1.

SEQ ID NO: 64 is a TaqMan probe used to detect the yield of amplicongenerated using SEQ ID NOS: 62 and 63.

SEQ ID NO: 65 is a Sabin 2 cassette d (VP1 region) sequence with areduced number of CG dinucleotides.

SEQ ID NO: 66 is a Sabin 2 cassette d (VP1 region) sequence with areduced number of CG and TA dinucleotides.

SEQ ID NO: 67 is a Sabin 2 cassette d (VP1 region) sequence with anincreased number of CG dinucleotides.

SEQ ID NO: 68 is a Sabin 2 cassette d (VP1 region) sequence with anincreased number of CG and TA dinucleotides.

SEQ ID NO: 69 is an exemplary deoptimized Sabin 2 cassette d (VP1region) sequence.

SEQ ID NO: 70 is a Sabin 2 cassette d (VP1 region) sequence that usesMEF1 codons for Sabin 2 amino acids.

DETAILED DESCRIPTION OF SEVERAL EMBODIMENTS Abbreviations and Terms

The following explanations of terms and methods are provided to betterdescribe the present disclosure and to guide those of ordinary skill inthe art in the practice of the present disclosure. The singular forms“a,” “an,” and “the” refer to one or more than one, unless the contextclearly dictates otherwise. For example, the term “comprising a nucleicacid molecule” includes single or plural nucleic acid molecules and isconsidered equivalent to the phrase “comprising at least one nucleicacid molecule.” The term “or” refers to a single element of statedalternative elements or a combination of two or more elements, unlessthe context clearly indicates otherwise. As used herein, “comprises”means “includes.” Thus, “comprising an alteration in the number of TA orCG dinucleotides,” means “including an alteration in the number of TAdinucleotides, the number of CG dinucleotides, or the number of CG andTA dinucleotides,” without excluding additional elements.

Unless explained otherwise, all technical and scientific terms usedherein have the same meaning as commonly understood to one of ordinaryskill in the art to which this disclosure belongs. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present disclosure, suitable methods andmaterials are described below. The materials, methods, and examples areillustrative only and not intended to be limiting.

OPV: oral poliovirus vaccine

PV: poliovirus

VAPP: vaccine-associated paralytic poliomyelitis

VDPV: vaccine-derived poliovirus

Adjuvant: A compound, composition, or substance that when used incombination with an immunogenic agent augments or otherwise alters ormodifies a resultant immune response. In some examples, an adjuvantincreases the titer of antibodies induced in a subject by theimmunogenic agent. In another example, if the antigenic agent is amultivalent antigenic agent, an adjuvant alters the particular epitopicsequences that are specifically bound by antibodies induced in asubject.

Exemplary adjuvants include, but are not limited to, Freund's IncompleteAdjuvant (IFA), Freund's complete adjuvant, B30-MDP, LA-15-PH,montanide, saponin, aluminum salts such as aluminum hydroxide (Amphogel,Wyeth Laboratories, Madison, N.J.), alum, lipids, keyhole limpetprotein, hemocyanin, the MF59 microemulsion, a mycobacterial antigen,vitamin E, non-ionic block polymers, muramyl dipeptides, polyanions,amphipatic substances, ISCOMs (immune stimulating complexes, such asthose disclosed in European Patent EP 109942), vegetable oil, Carbopol,aluminium oxide, oil-emulsions (such as Bayol F or Marcol 52), E. coliheat-labile toxin (LT), Cholera toxin (CT), and combinations thereof.

In one example, an adjuvant includes a DNA motif that stimulates immuneactivation, for example the innate immune response or the adaptiveimmune response by T-cells, B-cells, monocytes, dendritic cells, andnatural killer cells. Specific, non-limiting examples of a DNA motifthat stimulates immune activation include CG oligodeoxynucleotides, asdescribed in U.S. Pat. Nos. 6,194,388; 6,207,646; 6,214,806; 6,218,371;6,239,116; 6,339,068; 6,406,705; and 6,429,199, and IL-2 or otherimmunomodulators.

Administration: To provide or give a subject an agent, such as animmunogenic composition disclosed herein, by any effective route.Exemplary routes of administration include, but are not limited to,oral, injection (such as subcutaneous, intramuscular, intradermal,intraperitoneal, and intravenous), sublingual, rectal, transdermal,intranasal, vaginal, intraocular, and inhalation routes.

Agent: Any substance, including, but not limited to, a chemicalcompound, molecule, peptidomimetic, pathogen, or protein.

Antibody: A molecule including an antigen binding site whichspecifically binds (immunoreacts with) an antigen. Examples includepolyclonal antibodies, monoclonal antibodies, humanized monoclonalantibodies, or immunologically effective portions thereof.

Includes immunoglobulin molecules and immunologically active portionsthereof. Immunoglobulin genes include the kappa, lambda, alpha, gamma,delta, epsilon, and mu constant region genes, as well as the myriadimmunoglobulin variable region genes. Light chains are classified aseither kappa or lambda. Heavy chains are classified as gamma, mu, alpha,delta, or epsilon, which in turn define the immunoglobulin classes, IgG,IgM, IgA, IgD and IgE, respectively.

Antigen: A compound, composition, or substance that can stimulate theproduction of antibodies or a T-cell response in an animal, includingcompositions that are injected or absorbed into an animal. An antigenreacts with the products of specific humoral or cellular immunity,including those induced by heterologous immunogens. The term “antigen”includes all related antigenic epitopes. In one example, an antigen isan attenuated pathogen.

Attenuated pathogen: A pathogen with a decreased or weakened ability toproduce disease while retaining the ability to stimulate an immuneresponse like that of the natural pathogen. In one example, a livepathogen is attenuated by deoptimizing one or more codons in one or moregenes, such as an immunogenic surface antigen or a housekeeping gene. Inanother example, a pathogen is attenuated by selecting for avirulentvariants under certain growth conditions (for example see Sabin andBoulger. J. Biol. Stand. 1:115-8; 1973; Sutter et al., 2003. Poliovirusvaccine—live, p. 651-705. In S. A. Plotkin and W. A. Orenstein (ed.),Vaccines, Fourth ed. W.B. Saunders Company, Philadelphia).

Codons can be deoptimized, for example, by manipulating the nucleic acidsequence using molecular biology methods. Attenuated pathogens, such asan attenuated virus or bacterium, can be used in an immune compositionto stimulate an immune response in a subject. For example, attenuatedpathogens can be used in an attenuated vaccine to produce an immuneresponse without causing the severe effects of the disease. Particularexamples of attenuated vaccines include, but are not limited to,measles, mumps, rubella, polio, typhoid, yellow fever, and varicellavaccines.

cDNA (complementary DNA): A piece of DNA lacking internal, non-codingsegments (introns) and regulatory sequences that determinetranscription. cDNA can be synthesized in the laboratory by reversetranscription from messenger RNA or viral extracted from cells orpurified viruses.

Cellular immunity: An immune response mediated by cells or the productsthey produce, such as cytokines, rather than by an antibody. Itincludes, but is not limited to, delayed type hypersensitivity andcytotoxic T cells.

CG dinucleotide: A cytosine nucleotide immediately followed by a guaninein a nucleic acid sequence. Similarly, a TA (or UA) dinucleotide is athymine (or uracil) nucleotide immediately followed by a adenine in anucleic acid sequence. For example, the sequence GTAGTCGACT (nucleotides1-10 of SEQ ID NO: 2) has one CG dinucleotide and one TA dinucleotide(underlined).

Codon: A specific sequence of three adjacent nucleotide bases on astrand of DNA or RNA that provides genetic code information for aparticular amino acid or a termination signal.

Conservative substitution: One or more amino acid substitutions foramino acid residues having similar biochemical properties. Typically,conservative substitutions have little to no impact on the activity of aresulting polypeptide. For example, a conservative substitution is anamino acid substitution in an antigenic epitope of a pathogenic peptidethat does not substantially affect the ability of an antibody thatspecifically binds to the unaltered epitope to specifically bind theepitope including the conservative substitution. Thus, in some examples,a conservative variant of an epitope is also a functional variant of theepitope.

Methods which can be used to determine the amount of recognition by avariant epitope are disclosed herein. In addition, an alanine scan canbe used to identify which amino acid residues in a pathogenic epitopecan tolerate an amino acid substitution. In one example, recognition isnot decreased by more than 25%, for example not more than 20%, forexample not more than 10%, when an alanine, or other conservative aminoacid (such as those listed below), is substituted for one or more nativeamino acids. Similarly, an ELISA assay can be used that compares a levelof specific binding of an antibody that specifically binds a particularantigenic peptide to a level of specific binding of the antibody to acorresponding peptide with the substitution(s) to determine if thesubstitution(s) does not substantially affect specific binding of thesubstituted peptide to the antibody.

In one example, one, two, three, five, or ten conservative substitutionsare included in the peptide. In another example, 1-10 conservativesubstitutions are included in the peptide. In a further embodiment, atleast 2 conservative substitutions are included in the peptide. Apeptide can be produced to contain one or more conservativesubstitutions by manipulating the nucleotide sequence that encodes thatpolypeptide using, for example, standard procedures such assite-directed mutagenesis or PCR. Alternatively, a polypeptide can beproduced to contain one or more conservative substitutions by usingstandard peptide synthesis methods.

Substitutional variants are those in which at least one residue in theamino acid sequence has been removed and a different residue inserted inits place. Conservative substitution tables providing functionallysimilar amino acids are well known in the art. Examples of amino acidswhich may be substituted for an original amino acid in a protein andwhich are regarded as conservative substitutions include: Ser for Ala;Lys for Arg; Gln or His for Asn; Glu for Asp; Ser for Cys; Asn for Gln;Asp for Glu; Pro for Gly; Asn or Gln for His; Leu or Val for Ile; Ile orVal for Leu; Arg or Gln for Lys; Leu or Ile for Met; Met, Leu or Tyr forPhe; Thr for Ser; Ser for Thr; Tyr for Trp; Trp or Phe for Tyr; and Ileor Leu for Val.

Further information about conservative substitutions can be found, amongother sources, Ben-Bassat et al., (J. Bacteriol. 169:751-7, 1987),O'Regan et al., (Gene 77:237-51, 1989), Sahin-Toth et al., (Protein Sci.3:240-7, 1994), Hochuli et al., (Bio/Technology 6:1321-5, 1988) and instandard textbooks of genetics and molecular biology.

DNA (deoxyribonucleic acid): A long chain polymer which includes thegenetic material of most living organisms (many viruses have genomescontaining only ribonucleic acid, RNA). The repeating units in DNApolymers are four different nucleotides, each of which includes one ofthe four bases, adenine, guanine, cytosine and thymine bound to adeoxyribose sugar to which a phosphate group is attached. Triplets ofnucleotides, referred to as codons, in DNA molecules code for amino acidin a polypeptide. The term codon is also used for the corresponding (andcomplementary) sequences of three nucleotides in the mRNA into which theDNA sequence is transcribed.

Degenerate variant: A nucleic acid sequence encoding a peptide thatincludes a sequence that is degenerate as a result of the genetic code.There are 20 natural amino acids, most of which are specified by morethan one of the 61 codons of the “universal” genetic code used by mostcells and viruses. For example, the amino acid Ala is encoded by fourcodon triplets: GCU, GCG, GCA, and GCC. Therefore, all degeneratenucleotide sequences are included as long as the amino acid sequence ofthe peptide encoded by the nucleotide sequence is unchanged.

Deoptimization of a codon: To replace a preferred codon in a nucleicacid sequence with a synonymous codon (one that codes for the same aminoacid) less frequently used (unpreferred) in the organism. Each organismhas a particular codon usage bias for each amino acid, which can bedetermined from publicly available codon usage tables (for example seeNakamura et al., Nucleic Acids Res. 28:292, 2000 and references citedtherein; Sharp et al., Nucleic Acids Res. 16:8207-11, 1988; Chou andZhang, AIDS Res. Hum. Retroviruses. December; 8(12):1967-76, 1992; Westand Iglewski et al., Nucleic Acids Res. 16:9323-35, 1988, Rothberg andWimmer, Nucleic Acids Res. 9:6221-9, 1981; Jenkins et al., J. Mol. Evol.52:383-90, 2001; and Watterson, Mol. Biol. Evol. 9:666-77, 1992; allherein incorporated by reference). In addition, codon usage tables areavailable for several organisms on the internet at GenBank's website.

For example, if an organism has a codon usage for the amino acid Val of15% for GUU, 10% for GUC, 50% for GUA, and 25% for GUG, the “leastfrequently used codon” is GUC. Therefore, to deoptimize a Val codon, thecodon GUC could be used to replace one or more of the codons GUU, GUA,or GUG in a native sequence. Similarly, the codon GUU is a “lessfrequently used codon” than the GUA codon, and therefore, GUU could beused to replace GUA.

In some examples, the choice of the less frequently used codon is madedepending on whether the codon will alter the G+C content, the number ofCG dinucleotides, the number of TA(UA) dinucleotides, or combinationsthereof, in the deoptimized sequence. For example, if an organism has acodon usage for the amino acid Val of 50% for GUU, 10% for GUC, 15% forGUA, and 25% for GUG, the codon GUA is a “less frequently used codon”than the GUU codon, and could be used to replace GUU, for example if itwas desired to increase the number of UA (TA) dinucleotides in thedeoptimized sequence. Similarly, the codon GUG is a “less frequentlyused codon” than the GUU codon, and could be used to replace GUU, forexample if it was desired to increase the G+C content of the deoptimizedsequence.

Deoptimized pathogen: A pathogen having a nucleic acid coding sequencewith one or more deoptimized codons, which decrease the replicativefitness of the pathogen. In some examples, refers to the isolateddeoptimized nucleic acid sequence itself, independent of the pathogenicorganism.

Epitope: An antigenic determinant. Chemical groups or peptide sequenceson a molecule that are antigenic, that is, that elicit a specific immuneresponse. An antibody binds a particular antigenic epitope, or a T-cellreacts with a particular antigenic epitope bound to a specific MHCmolecule. In some examples, an epitope has a minimum sequence of 6-8amino acids, and a maximum sequence of about 100 amino acids, forexample, about 50, 25 or 18 amino acids in length.

Functional variant: Sequence alterations in a peptide, wherein thepeptide with the sequence alterations retains a function or property(such as immunogenicity) of the unaltered peptide. For example, afunctional variant of an epitope can specifically bind an antibody thatbinds an unaltered form of the epitope or stimulates T-cellproliferation to an extent that is substantially the same as theunaltered form of the epitope. Sequence alterations that providefunctional variants can include, but are not limited to, conservativesubstitutions, deletions, mutations, frameshifts, and insertions. Assaysfor determining antibody binding and T-cell reactivity are well known inthe art.

Screens for immunogenicity can be performed using well known methodssuch as those described in Harlow and Lane, Antibodies: A LaboratoryManual, Cold Spring Harbor Laboratory, 1988, or in Paul, FundamentalImmunology, 3rd ed., 243-247 (Raven Press, 1993) and references citedtherein. For example, a peptide can be immobilized on a solid supportand contacted with subject sera to allow binding of antibodies withinthe sera to the immobilized polypeptide. Unbound sera may then beremoved and bound antibodies detected using, for example, ¹²⁵I-labeledProtein A. The ability of a functional variant to react withantigen-specific antisera may be unchanged relative to original epitope,or may be enhanced or diminished by less than 30%, for example, lessthan 20%, such as less than 10%, relative to the unaltered epitope.

G+C content: The amount of guanine (G) and cytosine (C) in a nucleicacid sequence (such as a pathogen coding sequence). In particularexamples, the amount can be expressed in mole fraction or percentage oftotal number of bases in the sequence. For example, the sequenceGTAGTCGACT (nucleotides 1-10 of SEQ ID NO: 2) would be said to have aG+C content of 50% (5 of the 10 bases are guanine and cytosine).

Humoral immunity: Immunity that can be transferred with immune serumfrom one subject to another. Typically, humoral immunity refers toimmunity resulting from the introduction of specific antibodies orstimulation of the production of specific antibodies, for example byadministration of one or more of the pathogens with decreasedreplicative fitness disclosed herein.

Hybridization: The binding of a nucleic acid molecule to another nucleicacid molecule, for example the binding of a single-stranded DNA or RNAto another nucleic acid, thereby forming a duplex molecule. The abilityof one nucleic acid molecule to bind to another nucleic acid moleculecan depend upon the complementarity between the nucleotide sequences oftwo nucleic acid molecules, and the stringency of the hybridizationconditions.

Methods of performing hybridization are known in the art (such as thosedescribed in sections 7.39-7.52 of Sambrook et al., (1989) MolecularCloning, second edition, Cold Spring Harbor Laboratory, Plainview,N.Y.). For example, Southern or Northern analysis can be used todetermine if one nucleic acid sequence hybridizes to another nucleicacid sequence.

Deoptimized nucleic acid molecules are disclosed herein, such as SEQ IDNOs: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54,55, 56, 57, 58, 67, 68, and 69. However, the present disclosureencompasses other deoptimized nucleic acid molecules that can hybridizeto any of SEQ ID NOs: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42,45, 48, 51, 54, 55, 56, 57, 58, 67, 68, or 69, under moderate or highstringent conditions. In some examples, sequences that can hybridize toany of SEQ ID NOs: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45,48, 51, 54, 55, 56, 57, 58, 67, 68, or 69 are at least 100 nucleotidesin length (such as at least 500, at least 750, at least 1000, at least2500, or at least 5000 nucleotides in length) and hybridize, undermoderate or high hybridization conditions, to the sense or antisensestrand of any of SEQ ID NOs: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36,39, 42, 45, 48, 51, 54, 55, 56, 57, 58, 67, 68, or 69.

Moderately stringent hybridization conditions are when the hybridizationis performed at about 42° C. in a hybridization solution containing 25mM KPO4 (pH 7.4), 5×SSC, 5× Denhart's solution, 50 μg/mL denatured,sonicated salmon sperm DNA, 50% formamide, 10% Dextran sulfate, and 1-15ng/mL probe (about 5×10⁷ cpm/μg), while the washes are performed atabout 50° C. with a wash solution containing 2×SSC and 0.1% sodiumdodecyl sulfate.

Highly stringent hybridization conditions are when the hybridization isperformed at about 42° C. in a hybridization solution containing 25 mMKPO₄ (pH 7.4), 5×SSC, 5× Denhart's solution, 50 μg/mL denatured,sonicated salmon sperm DNA, 50% formamide, 10% Dextran sulfate, and 1-15ng/mL probe (about 5×10⁷ cpm/μg), while the washes are performed atabout 65° C. with a wash solution containing 0.2×SSC and 0.1% sodiumdodecyl sulfate.

Immune response: A response of a cell of the immune system, such as aB-cell, T-cell, macrophage, monocyte, or polymorphonucleocyte, to animmunogenic agent (such as the disclosed pathogens having decreasedreplicative fitness or sequences therefrom) in a subject. An immuneresponse can include any cell of the body involved in a host defenseresponse, such as an epithelial cell that secretes interferon or acytokine. An immune response includes, but is not limited to, an innateimmune response or inflammation.

The response can be specific for a particular antigen (an“antigen-specific response”). In a particular example, an immuneresponse is a T cell response, such as a CD4+ response or a CD8+response. In another example, the response is a B cell response, andresults in the production of specific antibodies to the immunogenicagent.

In some examples, such an immune response provides protection for thesubject from the immunogenic agent or the source of the immunogenicagent. For example, the response can protect a subject, such as a humanor veterinary subject, from infection by a pathogen, or interfere withthe progression of an infection by a pathogen. An immune response can beactive and involve stimulation of the subject's immune system, or be aresponse that results from passively acquired immunity.

Immunity: The state of being able to mount a protective response uponexposure to an immunogenic agent (such as the disclosed pathogens havingdecreased replicative fitness or sequences therefrom). Protectiveresponses can be antibody-mediated or immune cell-mediated, and can bedirected toward a particular pathogen. Immunity can be acquired actively(such as by exposure to an immunogenic agent, either naturally or in apharmaceutical composition) or passively (such as by administration ofantibodies).

Immunogen: An agent (such as a compound, composition, or substance) thatcan stimulate or elicit an immune response by a subject's immune system,such as stimulating the production of antibodies or a T-cell response ina subject. Immunogenic agents include, but are not limited to, pathogens(such as the disclosed pathogens having decreased replicative fitness orsequences therefrom) and their corresponding proteins. One specificexample of an immunogenic composition is a vaccine.

Immunogenic carrier: An immunogenic macromolecule to which an antigenicmolecule (such as a pathogen with decreased replicative fitness) isbound. When bound to a carrier, the bound molecule becomes moreimmunogenic, such as an increase of at least 5%, at least 10%, at least20%, or even at least 50%. Carriers can be used to increase theimmunogenicity of the bound molecule or to elicit antibodies against thecarrier which are diagnostically, analytically, or therapeuticallybeneficial. Covalent linking of a molecule to a carrier confers enhancedimmunogenicity and T-cell dependence (Pozsgay et al., PNAS 96:5194-97,1999; Lee et al., J. Immunol. 116:1711-18, 1976; Dintzis et al., PNAS73:3671-75, 1976). Exemplary carriers include polymeric carriers, whichcan be natural (for example, polysaccharides, polypeptides or proteinsfrom bacteria or viruses), semi-synthetic or synthetic materialscontaining one or more functional groups to which a reactant moiety canbe attached.

Examples of bacterial products for use as carriers include, but are notlimited to, bacterial toxins, such as B. anthracis PA (includingfragments that contain at least one antigenic epitope and analogs orderivatives capable of eliciting an immune response), LF and LeTx, andother bacterial toxins and toxoids, such as tetanus toxin/toxoid,diphtheria toxin/toxoid, P. aeruginosa exotoxin/toxoid/, pertussistoxin/toxoid, and C. perfringens exotoxin/toxoid. Viral proteins, suchas hepatitis B surface antigen and core antigen can also be used ascarriers, as well as proteins from higher organisms such as keyholelimpet hemocyanin, horseshoe crab hemocyanin, edestin, mammalian serumalbumins, and mammalian immunoglobulins. Additional bacterial productsfor use as carriers include, but are not limited to, bacterial wallproteins and other products (for example, streptococcal orstaphylococcal cell walls and lipopolysaccharide (LPS)).

Immunogenicity: The ability of an agent to induce a humoral or cellularimmune response. Immunogenicity can be measured, for example, by theability to bind to an appropriate MHC molecule (such as an MHC Class Ior II molecule) and to induce a T-cell response or to induce a B-cell orantibody response, for example, a measurable cytotoxic T-cell responseor a serum antibody response to a given epitope. Immunogenicity assaysare well-known in the art and are described, for example, in Paul,Fundamental Immunology, 3rd ed., 243-247 (Raven Press, 1993) andreferences cited therein.

Immunologically Effective Dose: A therapeutically effective amount of animmunogen (such as the disclosed pathogens having decreased replicativefitness or sequences therefrom) that will prevent, treat, lessen, orattenuate the severity, extent or duration of a disease or condition,for example, infection by a pathogen.

Isolated: An “isolated” biological component (such as, a nucleic acidmolecule or protein) has been substantially separated, produced apartfrom, or purified away from other biological components in the cell ofthe organism in which the component occurs, for example, otherchromosomal and extra-chromosomal DNA and RNA, and proteins. Nucleicacid molecules and proteins which have been “isolated” include nucleicacid molecules and proteins purified by standard purification methods.The term also embraces nucleic acid molecules and proteins prepared byrecombinant expression in a host cell as well as chemically synthesizedproteins and nucleic acids. Samples of isolated biological componentsinclude samples of the biological component wherein the biologicalcomponent represents greater than 90% (for example, greater than 95%,such as greater than 98%) of the sample.

An “isolated” microorganism (such as a virus, bacterium, fungus, orprotozoa) has been substantially separated or purified away frommicroorganisms of different types, strains, or species. Microorganismscan be isolated by a variety of techniques, including serial dilutionand culturing.

Lymphocytes: A type of white blood cell involved in the immune defensesof the body. There are two main types of lymphocytes: B-cells andT-cells.

Mimetic: A molecule (such as an organic chemical compound) that mimicsthe activity of another molecule.

Nucleic acid molecule: A deoxyribonucleotide or ribonucleotide polymerincluding, without limitation, cDNA, mRNA, genomic DNA, genomic RNA, andsynthetic (such as chemically synthesized) DNA. Includes nucleic acidsequences that have naturally-occurring, modified, ornon-naturally-occurring nucleotides linked together bynaturally-occurring or non-naturally-occurring nucleotide linkages.Nucleic acid molecules can be modified chemically or biochemically andcan contain non-natural or derivatized nucleotide bases. Suchmodifications include, for example, labels, methylation, substitution ofone or more of the naturally occurring nucleotides with analogs, andinternucleotide linkage modifications.

Nucleic acid molecules can be in any topological conformation, includingsingle-stranded, double-stranded, partially duplexed, triplexed,hairpinned, circular, linear, and padlocked conformations. Wheresingle-stranded, a nucleic acid molecule can be the sense strand or theantisense strand. Also included are synthetic molecules that mimicpolynucleotides in their ability to bind to a designated sequence viahydrogen bonding and other chemical interactions. Such molecules areknown and include, for example, molecules in which peptide linkages aresubstituted for phosphate linkages in the backbone.

The disclosure includes isolated nucleic acid molecules that includespecified lengths of a nucleotide sequence. Such molecules can includeat least 10, at least 15, at least 20, at least 25, at least 30, atleast 35, at least 40, at least 45, at least 50, at least 100, at least300 or at least 500 nucleotides of these sequences or more, and can beobtained from any region of a nucleic acid molecule.

Nucleotide: A subunit of DNA or RNA including a nitrogenous base(adenine, guanine, thymine, or cytosine in DNA; adenine, guanine,uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule(deoxyribose in DNA and ribose in RNA).

Passive immunity: Immunity acquired by the introduction by immune systemcomponents into a subject rather than by stimulation.

Pathogen: A disease-producing agent. Examples include, but are notlimited to microbes such as viruses, bacteria, fungi, and protozoa.

Peptide, polypeptide, and protein: Polymers of amino acids (typicallyL-amino acids) or amino acid mimetics linked through peptide bonds orpeptide bond mimetic to form a chain. The terminal amino acid at one endof the chain typically has a free amino group (the amino-terminus),while the terminal amino acid at the other end of the chain typicallyhas a free carboxyl group (the carboxy terminus). Encompasses any aminoacid sequence and includes modified sequences such as glycoproteins. Theterms cover naturally occurring proteins, as well as those which arerecombinantly or synthetically produced.

As used herein, the terms are interchangeable since they all refer topolymers of amino acids (or their analogs) regardless of length.Non-natural combinations of naturally- or non-naturally occurringsequences of amino acids may also be referred to as “fusion proteins.”

Pharmaceutically Acceptable Carriers: The pharmaceutically acceptablecarriers (vehicles) useful in this disclosure are conventional.Remington's Pharmaceutical Sciences, by E. W. Martin, Mack PublishingCo., Easton, Pa., 15th Edition (1975), describes compositions andformulations suitable for pharmaceutical delivery of one or moretherapeutic compounds or molecules, such as one or more nucleic acidmolecules, proteins or immunogenic compositions disclosed herein.

In general, the nature of the carrier will depend on the particular modeof administration being employed. For instance, parenteral formulationscan include injectable fluids that include pharmaceutically andphysiologically acceptable fluids such as water, physiological saline,balanced salt solutions, aqueous dextrose, glycerol or the like as avehicle. In addition to biologically-neutral carriers, pharmaceuticalcompositions to be administered can contain minor amounts of non-toxicauxiliary substances, such as wetting or emulsifying agents,preservatives, and pH buffering agents and the like, for example sodiumacetate or sorbitan monolaurate, sodium lactate, potassium chloride,calcium chloride, and triethanolamine oleate.

Poliovirus (PV): An enterovirus of the Picornaviridae family that is thecausative agent of poliomyelitis (polio).

Purified: The term purified does not require absolute purity; rather, itis intended as a relative term. Thus, for example, a purified peptidepreparation is one in which the peptide is more enriched than thepeptide is in its natural environment within a cell or cell extract. Inone example, a preparation is purified such that the purified peptiderepresents at least 50% of the total peptide content of the preparation.In other examples, a peptide is purified to represent at least 90%, suchas at least 95%, or even at least 98%, of all macromolecular speciespresent in a purified preparation prior to admixture with otherformulation ingredients, such as a pharmaceutical carrier, excipient,buffer, absorption enhancing agent, stabilizer, preservative, adjuvantor other co-ingredient. In some examples, the purified preparation is beessentially homogeneous, wherein other macromolecular species are notdetectable by conventional techniques.

Such purified preparations can include materials in covalent associationwith the active agent, such as glycoside residues or materials admixedor conjugated with the active agent, which may be desired to yield amodified derivative or analog of the active agent or produce acombinatorial therapeutic formulation, conjugate, fusion protein or thelike. The term purified thus includes such desired products as peptideand protein analogs or mimetics or other biologically active compoundswherein additional compounds or moieties are bound to the active agentin order to allow for the attachment of other compounds or provide forformulations useful in therapeutic treatment or diagnostic procedures.

Quantitating: Determining a relative or absolute quantity of aparticular component in a sample. For example, in the context ofquantitating antibodies in a sample of a subject's blood to detectinfection by a pathogen, quantitating refers to determining the quantityof antibodies using an antibody assay, for example, an ELISA-assay or aT-cell proliferation assay.

Recombinant: A recombinant nucleic acid molecule is one that has asequence that is not naturally occurring or has a sequence that is madeby an artificial combination of two otherwise separated segments ofsequence. This artificial combination can be accomplished by chemicalsynthesis or by the artificial manipulation of isolated segments ofnucleic acids, for example, by genetic engineering techniques such asthose described in Sambrook et al. (ed.), Molecular Cloning: ALaboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1989. The term recombinant includesnucleic acid molecules that have been altered solely by addition,substitution, or deletion of a portion of the nucleic acid molecule.Similarly, a recombinant protein is one encoded for by a recombinantnucleic acid molecule.

Replicative fitness: The ability of a pathogen to produce matureinfectious progeny. In some examples, introduction of one or moredeoptimized codons into a pathogen reduces the replicative fitness ofthe pathogen, as compared to a pathogen containing native codons. Inparticular examples, introduction of one or more deoptimized codons intoa pathogen, in combination with altering the G+C content or altering thenumber of CG or TA dinucleotides in a coding sequence, reduces thereplicative fitness of the pathogen, as compared to a pathogencontaining native codons. In some examples, such replicative fitness isreduced by at least 10%, such as at least 20%, at least 50%, or even atleast 90% as compared to a pathogen containing native codons.

Methods that can be used to determine replicative fitness are disclosedherein and are known in the art. For example, to determine thereplicative fitness of a virus, plaque size can be determined,infectious center assays can be used, viral titer by TCID50(tissue-culture infectious doses 50%) or plaque assay, replication insingle-step growth curves, temperature-sensitivity or cold-sensitivityof plaques determined, unusual host range observed, or competitionassays with a related virus can be determined. To determine thereplicative fitness of a bacterium or fungus, exemplary replicativefitness assays include assays for colony-forming activity,temperature-sensitivity, cold-sensitivity, slow growth under certainconditions, increased or rapid bacterial death, reduced ability of thebacteria or fungi to survive various stress conditions (such as nutrientdeprivation), altered host range, enzymatic assays indicating reducedactivity of a key enzyme, or assays for reduced pathogenicity due todecreased expression of an important protein (such as LPS).

Specific Binding Agent: An agent that binds substantially only to adefined target. Thus a protein-specific binding agent bindssubstantially only the defined protein, or to a specific region withinthe protein. As used herein, a specific binding agent includesantibodies and other agents that bind substantially to a specifiedpeptide.

The determination that a particular agent binds substantially only to aspecific peptide can readily be made by using or adapting routineprocedures. One suitable in vitro assay makes use of the Westernblotting procedure (described in many standard texts, including Harlowand Lane, Using Antibodies: A Laboratory Manual, CSHL, New York, 1999).

Specifically bind: Refers to the ability of a particular agent (a“specific binding agent”) to specifically react with a particularanalyte, for example to specifically immunoreact with an antibody, or tospecifically bind to a particular peptide sequence. The binding is anon-random binding reaction, for example between an antibody moleculeand an antigenic determinant. Binding specificity of an antibody istypically determined from the reference point of the ability of theantibody to differentially bind the specific antigen and an unrelatedantigen, and therefore distinguish between two different antigens,particularly where the two antigens have unique epitopes. An antibodythat specifically binds to a particular epitope is referred to as a“specific antibody”.

In particular examples, two compounds are said to specifically bind whenthe binding constant for complex formation between the componentsexceeds about 10⁴ L/mol, for example, exceeds about 10⁶ L/mol, exceedsabout 10⁸ L/mol, or exceeds about 10¹⁰ L/mol. The binding constant fortwo components can be determined using methods that are well known inthe art.

Subject: Living multi-cellular organisms, a category that includes humanand non-human mammals, as well as other veterinary subjects such as fishand birds.

Therapeutically effective amount: An amount of a therapeutic agent (suchas an immunogenic composition) that alone, or together with anadditional therapeutic agent(s), induces the desired response, such as aprotective immune response or therapeutic response to a pathogen. In oneexample, it is an amount of immunogen needed to increase resistance to,prevent, ameliorate, or treat infection and disease caused by apathogenic infection in a subject. Ideally, a therapeutically effectiveamount of an immunogen is an amount sufficient to increase resistanceto, prevent, ameliorate, or treat infection and disease caused by apathogen without causing a substantial cytotoxic effect in the subject.The preparations disclosed herein are administered in therapeuticallyeffective amounts.

In general, an effective amount of a composition administered to a humanor veterinary subject will vary depending upon a number of factorsassociated with that subject, for example whether the subject previouslyhas been exposed to the pathogen. An effective amount of a compositioncan be determined by varying the dosage of the product and measuring theresulting immune or therapeutic responses, such as the production ofantibodies. Effective amounts also can be determined through various invitro, in vivo or in situ immunoassays. The disclosed therapeutic agentscan be administered in a single dose, or in several doses, as needed toobtain the desired response. However, the effective amount of can bedependent on the source applied, the subject being treated, the severityand type of the condition being treated, and the manner ofadministration.

The disclosed therapeutic agents can be administered alone, or in thepresence of a pharmaceutically acceptable carrier, or in the presence ofother agents, for example an adjuvant.

In one example, a desired response is to increase an immune response inresponse to infection with a pathogen. For example, the therapeuticagent can increase the immune response by a desired amount, for exampleby at least 5%, at least 10%, at least 15%, at least 20%, at least 25%,at least 30%, at least 50%, at least 75%, or even at least 90%, ascompared to an immune response in the absence of the therapeutic agent.This increase can result in decreasing or slowing the progression of, adisease or condition associated with a pathogenic infection.

In another example, a desired response is to decrease the incidence ofvaccine-associated paralytic poliomyelitis in response to an attenuatedSabin oral polio vaccine. The incidence of vaccine-associated paralyticpoliomyelitis does not need to be completely eliminated for atherapeutic agent, such as a pharmaceutical preparation that includes animmunogen, to be effective. For example, the therapeutic agent (such asa codon-deoptimized oral polio vaccine) can decrease the incidence ofvaccine-associated paralytic poliomyelitis or the emergence ofcirculating vaccine-derived polioviruses by a desired amount, forexample by at least 5%, at least 10%, at least 15%, at least 20%, atleast 25%, at least 30%, at least 50%, at least 75%, or even at least90%, as compared to the incidence of vaccine-associated paralyticpoliomyelitis or the emergence of circulating vaccine-derivedpolioviruses in the presence of a oral polio vaccine containing nativecodons.

Treating a disease: “Treatment” refers to a therapeutic interventionthat ameliorates a sign or symptom of a disease or pathologicalcondition related to a disease, even if the underlying pathophysiologyis not affected. Reducing a sign or symptom associated with a pathogenicinfection can be evidenced, for example, by a delayed onset of clinicalsymptoms of the disease in a susceptible subject, a reduction inseverity of some or all clinical symptoms of the disease, a slowerprogression of the disease, a reduction in the number of relapses of thedisease, an improvement in the overall health or well-being of thesubject, or by other parameters well known in the art that are specificto the particular disease.

Treatment can also induce remission or cure of a condition, such as apathogenic infection or a pathological condition associated with such aninfection. In particular examples, treatment includes preventing adisease, for example by inhibiting or even avoiding altogether the fulldevelopment of a disease or condition, such as a disease associated witha pathogen, such as polio. Thus, prevention of pathogenic disease caninclude reducing the number of subjects who acquire a disease associatedwith a pathogenic infection (such as the development of polio orpoliomyelitis by the polio virus or development of rabies by the rabiesvirus) in a population of subjects receiving a preventative treatment(such as vaccination) relative to an untreated control population, ordelaying the appearance of such disease in a treated population versusan untreated control population. Prevention of a disease does notrequire a total absence of disease. For example, a decrease of at least50% can be sufficient.

Unit dose: A physically discrete unit containing a predeterminedquantity of an active material calculated to individually orcollectively produce a desired effect such as an immunogenic effect. Asingle unit dose or a plurality of unit doses can be used to provide thedesired effect, such as an immunogenic effect. In one example, a unitdose includes a desired amount of one or more of the disclosed pathogenshaving reduced replicative fitness.

Vaccine: An immunogenic composition that can be administered to ananimal or a human to confer immunity, such as active immunity, to adisease or other pathological condition. Vaccines can be usedprophylactically or therapeutically. Thus, vaccines can be used reducethe likelihood of infection or to reduce the severity of symptoms of adisease or condition or limit the progression of the disease orcondition. In one example, a vaccine includes one or more of thedisclosed pathogens having reduced replicative fitness.

Vector: A nucleic acid molecule as introduced into a host cell, therebyproducing a transformed host cell. A vector can include nucleic acidsequences that permit it to replicate in the host cell, such as anorigin of replication. A vector can also include one or more therapeuticgenes or selectable marker genes and other genetic elements known in theart. A vector can transduce, transform or infect a cell, thereby causingthe cell to express nucleic acid molecules or proteins other than thosenative to the cell. A vector optionally includes materials to aid inachieving entry of the nucleic acid into the cell, such as a viralparticle, liposome, protein coating or the like. In one example, avector is a viral vector. Viral vectors include, but are not limited to,retroviral and adenoviral vectors.

Deoptimizing Codon Usage to Decrease Replicative Fitness

This disclosure provides methods of decreasing the replicative fitnessof a pathogen by deoptimizing codon usage in one or more genes of thepathogen. Such methods can be used to increase the genetic stability ofthe attenuated phenotype of currently available attenuated vaccines, aswell as to generate new attenuated pathogens that can be used inimmunogenic compositions. For example, the attenuated Sabin oral poliovaccine (OPV) strains are genetically unstable. This instability is theunderlying cause of vaccine-associated paralytic poliomyelitis and theemergence of circulating vaccine-derived polioviruses. Therefore, thedisclosed compositions and methods can be used to reduce the incidenceof vaccine-associated paralytic poliomyelitis and other disorders causedby currently available live attenuated vaccines. The disclosed methodsand compositions increase the genetic stability of pathogens bydistributing attenuating mutations over many sites within the pathogen'sgenome.

Codon usage bias, the use of synonymous codons at unequal frequencies,is ubiquitous among genetic systems (Ikemura, J. Mol. Biol. 146:1-21,1981; Ikemura, J. Mol. Biol. 158:573-97, 1982). The strength anddirection of codon usage bias is related to genomic G+C content and therelative abundance of different isoaccepting tRNAs (Akashi, Curr. Opin.Genet. Dev. 11:660-6, 2001; Duret, Curr. Opin. Genet. Dev. 12:640-9,2002; Osawa et al., Microbiol. Rev. 56:229-64, 1992). Codon usage canaffect the efficiency of gene expression. In Escherichia coli (Ikemura,J. Mol. Biol. 146:1-21, 1981; Xia Genetics 149:37-44, 1998),Saccharomyces cerevisiae (Bennetzen and Hall, J. Biol. Chem.257:3026-31, 1982; Ikemura, J. Mol. Biol. 158:573-97, 1982),Caenorhabditis elegans (Duret, Curr. Opin. Genet. Dev. 12:640-9, 2002),Drosophila melanogaster (Moriyama and Powell, J. Mol. Evol. 45:514-23,1997), and Arabidopsis thaliana (Chiapello et al. Gene 209:GC1-GC38,1998) the most highly expressed genes use codons matched to the mostabundant tRNAs (Akashi and Eyre-Walker, Curr. Opin. Genet. Dev.8:688-93, 1998). By contrast, in humans and other vertebrates, codonusage bias is more strongly correlated with the G+C content of theisochore where the gene is located (Musto et al., Mol. Biol. Evol.18:1703-7, 2001; Urrutia and Hurst, Genetics 159:1191-9, 2001) than withthe breadth or level of gene expression (Duret, Curr. Opin. Genet. Dev.12:640-9, 2002) or the number of tRNA genes (Kanaya et al., J. Mol.Evol. 53:290-8, 2001).

The deoptimized nucleic acid sequences of the present applicationinclude one or more codons that are degenerate as a result of thegenetic code. There are 20 natural amino acids, most of which arespecified by more than one codon. However, organisms have codons whichare used more frequently, and those that are used less frequently(deoptimized). All possible deoptimized nucleotide sequences areincluded in the disclosure as long as the deoptimized nucleotidesequence retains the ability to decrease replicative fitness, forexample by at least 10%, at least 20%, at least 50% or even at least 75%as compared to the replicative fitness of a pathogen with a codonoptimized nucleic acid sequence.

Optimization of codon composition is frequently required for efficientexpression of genes in heterologous host systems (André et al., J.Virol. 72:1497-503, 1998; Kane, Curr. Opin. Biotech. 6:494-500, 1995;Smith, Biotech. Prog. 12:417-22, 1996; Yadava and Ockenhouse. Infect.Immun. 71:4961-9, 2003). Conversely, engineered codon deoptimization candramatically decrease the efficiency of gene expression in severalorganisms (Robinson et al., Nucleic Acids Res. 12:6663-71, 1984; Hoekemaet al., Mol. Cell Biol. 7:2914-24, 1987; Carlini and Stephan. Genetics163:239-43, 2003; and Zhou et al., J. Virol. 73:4972-82, 1999). However,it has not been previously taught or suggested that deoptimization ofsequences of a microbial pathogen (such as a housekeeping or antigenicsequence) could be used to systematically reduce the replicative fitnessof the pathogen, thereby producing a novel approach for developingattenuated derivatives of the pathogen having well-defined levels ofreplicative fitness, and increasing the genetic stability of theattenuated phenotype.

Selection of Codons to Deoptimize

The methods provided herein include deoptimizing at least one codon in acoding sequence of a pathogen, thereby generating a deoptimized codingsequence. Such deoptimization reduces replicative fitness of thepathogen. In particular examples, methods of reducing the replicativefitness of a pathogen include identifying one or more amino acids thatare encoded by at least 2 different codons in the pathogen (such as 2different codons, 3 different codons, 4 different codons, or 6 differentcodons). In some examples, the codon used least frequently (lowest codonusage frequency) for a particular amino acid is incorporated into thesequence of the pathogen (to replace the appropriate one or more codonsin the native sequence), thereby deoptimizing the pathogen sequence andreducing the replicative fitness of the pathogen. In other examples, acodon used with a lower frequency than at least one other codon (but notnecessarily the codon with the lowest frequency) for a particular aminoacid is incorporated into the sequence of the pathogen (to replace theappropriate one or more codons in the native sequence), for example toalter the G+C content of the sequence or alter the number of CG or TAdinucleotides in the sequence, thereby deoptimizing the pathogensequence and reducing the replicative fitness of the pathogen.Identification of infrequently used codons can be made by analyzing oneor more codon usage tables for the pathogen. The codon usage table usedcan include codon usage data from the complete genome of the pathogen(or 2 or more genomes, for example from different strains of thepathogen), codon usage data from one or more genes (such as 1 gene, atleast 2 genes, at least 3 genes, at least 5 genes, or even at least 10genes), for example one or more genes involved in the antigenicity ofthe pathogen. Codon usage tables are publicly available for a widevariety of pathogens (for example see Nakamura et al., Nucleic AcidsRes. 28:292, 2000; Sharp et al., Nucleic Acids Res. 16:8207-11, 1988;Chou and Zhang, AIDS Res. Hum. Retroviruses. December; 8(12):1967-76,1992; West and Iglewski et al., Nucleic Acids Res. 16:9323-35, 1988,Rothberg and Wimmer, Nucleic Acids Res. 9:6221-9, 1981; Jenkins et al.,J. Mol. Evol. 52:383-90, 2001; and Watterson, Mol. Biol. Evol. 9:666-77,1992; all herein incorporated by reference).

For example, if the pathogen uses the ACU, ACC, ACA, and ACG codons toencode for Thr at 45, 24, 20 and 11% frequency respectively, the ACGcodon can be chosen to replace at least one ACU, ACC, or ACA codonsequence of the native pathogen sequence, thereby generating adeoptimized sequence. This selection would also increase the number ofCG dinucleotides in the deoptimized sequence. However, if it was desiredto decrease the G+C content of the deoptimized sequence, the ACA codon(for example instead of ACG) can be chosen to replace the ACU codon. Inexamples where the amino acid is encoded by only two different codons,one of the two codons can be selected and used in the deoptimizedsequence if the codon usage is highly biased, such as a difference of atleast 10%, at least 20%, or at least 30%. For example, if the pathogenuses the codons UAU and UAC to encode for Tyr at 90% and 10% frequencyrespectively, the UAC codon is used to replace at least one UAU codon ofthe native pathogen sequence, thereby generating a deoptimized sequence.In contrast, if the pathogen uses the codons UAU and UAC to encode forTyr at 49% and 51% frequency respectively, Tyr codons would not likelybe chosen as the codons to deoptimize.

In some examples, there may be two or more codons used at lowfrequencies that are similar in value, such as codon usages that arewithin 0.01-2% of each other (for example within 0.1-2%, 0.5-2% or 1-2%of each other). In some examples, the codon with the lowest codon usagefrequency is not chosen to replace a codon more frequently used. In someexamples, the codon chosen is one that alters the G+C content of thedeoptimized sequence. In other examples, the codon chosen is one thatalters the frequency of a specific dinucleotide pair (such as CG or TA)found at low frequencies in that genome (such as no more than 3-4%). Oneexample is the CG dinucleotide, which is strongly suppressed inmammalian genomes and in the genomes of many RNA viruses (Karlin et al.,J. Virol. 68:2889-2897, 1994). Such dinucleotide pairs can fall acrosscodon boundaries, or be contained within the codon.

Reducing Replicative Fitness

The replicative fitness of a pathogen is the overall replicativecapacity of the pathogen to produce mature infectious progeny. Byintroducing one or more deoptimized codons into a coding region of apathogen's gene(s), the replicative fitness of the pathogen decreases.In some examples, replicative fitness is decreased by at least 10%, atleast 20%, at least 30%, at least 50%, at least 75%, at least 90%, atleast 95%, or even at least 98%, as compared to an amount of replicativefitness by the a pathogen of the same species and strain in the absenceof deoptimized codons. The disclosed methods can be used for makingvaccines because the replicative fitness of the pathogen can bemodulated by introducing different numbers of nucleotide changes. Thisflexibility can allow one to alter systematically the replicativefitness of a candidate vaccine strain in order to allow sufficientreplication to induce an immune response, but not enough replication tocause pathogenicity.

Methods that can be used to measure the replicative fitness of apathogen are known in the art and disclosed herein. For example, tomeasure the replicative fitness of a virus, plaque size can be measured,infectious center assays can be used, viral titer by TCID50(tissue-culture infectious doses 50%) or plaque assays can be used,replication in single-step growth curves can be determined,temperature-sensitivity or cold-sensitivity of plaques determined,determination of whether the virus has an unusual host range, orcompetition assays with a related virus can be determined. To determinethe replicative fitness of a bacterium or fungus, exemplary replicativefitness assays include assays for colony-forming activity,temperature-sensitivity, cold-sensitivity, slow growth under certainconditions, increased or rapid bacterial or fungal death, reducedability of the bacteria or fungi to survive various stress conditions(such as nutrient deprivation), altered host range, enzymatic assaysindicating reduced activity of a key enzyme, or assays for reducedpathogenicity due to decreased expression of an important protein (suchas LPS). To measure the replicative fitness of a protozoan, exemplaryreplicative fitness assays include competitive growth assays withunmodified homologues, temperature-sensitivity, cold-sensitivity, slowgrowth under certain conditions, increased or rapid senescence, reducedability to survive various stress conditions, altered host range,enzymatic assays indicating reduced activity of a key enzyme, or assaysfor reduced pathogenicity due to decreased expression of an importantprotein (such as surface antigens).

This disclosure provides several specific examples of pathogenscontaining deoptimized codons in various genes, including housekeepinggenes and genes encoding proteins that are determinants of immunity.However, one skilled in the art will understand how to use the disclosedmethods to deoptimize one or more codons in any pathogen of interestusing publicly available codon usage tables and publicly availablepathogen sequences In particular examples, a pathogen includes one ormore deoptimized codons, for example at least 2, at least 3, at least 4,at least 5, at least 6, at least 7, at least 8, at least 9, at least 10,at least 20, at least 50, at least 100, at least 200, at least 300, atleast 400, at least 500, at least 1000, or even at least 2000deoptimized codons.

In some examples, a pathogen includes deoptimization of at least 5% ofthe codons in a gene that encode a particular amino acid, such asdeoptimization of at least 5% of the codons that encode Ala (or anotheramino acid such as Leu, Thr, etc.), for example at least 10% of thecodons that encode Ala (or another amino acid), at least 20% of thecodons that encode Ala (or another amino acid), at least 50% of thecodons that encode Ala (or another amino acid), or at least 90% of thecodons that encode Ala (or another amino acid) in a gene. In particularexamples, a pathogen includes deoptimization of at least 5% of thecodons in one or more coding sequences, such as deoptimization of atleast 10%, at least 20%, at least 30%, at least 40%, at least 50%, atleast 60%, at least 70%, at least 80%, or even at least 90% of thecodons in one or more coding sequences.

In one example, viral pathogen sequences are deoptimized in one or morenucleic acid sequences that encode proteins encoding surface antigenswhich are determinants of immunity, such as a capsid sequences, or spikeglycoproteins.

In particular examples, deoptimizing the codon composition results in analtered G+C content of a coding sequence. For example, deoptimizing oneor more codons can increase or decrease the G+C content by at least 10%,such as increase the G+C content of a coding sequence by at least 10%,such as at least 20%, at least 30%, at least 40%, at least 50%, at least60%, at least 70%, at least 80%, or even by at least 90%, or decreasethe G+C content of a coding sequence by at least 10%, such as at least20%, at least 30%, at least 40%, at least 50%, at least 60%, at least70%, at least 80%, or even by at least 90%. Whether the G+C content isincreased or decreased will depend on the sequence of the pathogen ofinterest.

However, the G+C content can be deliberately altered in combination withdeoptimizing one or more codons in a pathogen sequence. For example,some of the nucleotide substitutions can be made to deoptimize codons,and other nucleotide substitutions can be made to alter the G+C contentof the sequence. Altering the G+C content of the sequence may alsoresult in a deoptimized codon, but is not required in all instances.

In one example, the pathogen is a rubella virus, whose RNA genome has ahigh G+C content. Therefore, deoptimization of rubella can be achievedby decreasing the G+C content of one or more coding sequences ofrubella, for example decreasing the G+C content by at least 10%, such asat least 20%, or even by at least 50%. In another example, the pathogenis a poliovirus or other eukaryotic virus, and deoptimization can beachieved by increasing the G+C content of one or more coding sequences,for example increasing the G+C content by at least 10%, such as at least20%, or even by at least 50%. Such changes in G+C content can beachieved as a result of deoptimizing one or more codons, or in additionto deoptimizing one or more codons.

In some examples, deoptimizing the codon composition results in analtered frequency (number) of CG dinucleotides, TA dinucleotides, orboth, in a coding sequence. For example, deoptimization of one or morecodons may increase or decrease the frequency of CG or TA dinucleotidesin the sequence by at least 10%, for example increase the number of CGor TA dinucleotides in a coding sequence by at least 10%, such as atleast 20%, at least 30%, at least 40%, at least 50%, at least 60%, atleast 100%, at least 200%, or even by at least 300%, or decrease in thenumber of CG or TA dinucleotides in a coding sequence by at least 10%,such as at least 20%, at least 30%, at least 40%, at least 50%, at least60%, at least 70%, at least 80%, or even by at least 90%. Whether thenumber of CG or TA dinucleotides is increased or decreased will dependon the sequence of the pathogen of interest.

However, the number of CG or TA dinucleotides can be deliberatelyaltered in combination with deoptimizing one or more codons in apathogen sequence. For example, some of the nucleotide substitutions canbe made to deoptimize codons, and other nucleotide substitutions can bemade to alter the number of CG or TA dinucleotides in the codingsequence. Altering the number of CG or TA dinucleotides in the sequencemay also result in a deoptimized codon, but is not required in allinstances.

In one example, the pathogen is a poliovirus or eukaryotic virus, anddeoptimization can be achieved by increasing the number of CG or TAdinucleotides in one or more coding sequences, for example increasingthe number of CG or TA dinucleotides by at least 10%, such as at least30%, or even by at least 300%. In another example, the pathogen is abacterium, and deoptimization can be achieved by decreasing the numberof CG or TA dinucleotides in one or more coding sequences, for exampledecreasing the number of CG or TA dinucleotides by at least 10%, such asat least 30%, or even by at least 50%.

In a particular example, the pathogen is a bacterium. Several methodscan be used to deoptimize one or more codons in bacterial codingsequences. For example, one or more codons can be deoptimized such thata single rare codon (such as AGG) is used to force exclusive AGG usagein the mRNA encoding the arginyl tRNA synthetase, potentially limitingthe pools of charged arginyl-tRNAs in the cell, and thereforesynergistically further limiting the production of arginyl tRNAsynthetase. In another example, one or more codons are deoptimized (forexample by exclusively using AGG to encode for Arg residues) in one ormore of the most highly expressed essential genes (such as translationfactors). In yet another example, the distribution of codon-deoptimizedgenes along the genome is chosen to reduce the likelihood that alldeoptimized genes could be exchanged out by any single naturalrecombination event.

Exemplary Pathogens

Any pathogen can be attenuated by deoptimizing one or more codons in oneor more coding sequences. Exemplary pathogens include, but are notlimited to, viruses, bacteria, fungi, and protozoa. For example, virusesinclude positive-strand RNA viruses and negative-strand RNA viruses.Exemplary positive-strand RNA viruses include, but are not limited to:Picornaviruses (such as Aphthoviridae [for examplefoot-and-mouth-disease virus (FMDV)]), Cardioviridae; Enteroviridae(such as Coxsackie viruses, Echoviruses, Enteroviruses, andPolioviruses); Rhinoviridae (Rhinoviruses)); Hepataviridae (Hepatitis Aviruses); Togaviruses (examples of which include rubella; alphaviruses(such as Western equine encephalitis virus, Eastern equine encephalitisvirus, and Venezuelan equine encephalitis virus)); Flaviviruses(examples of which include Dengue virus, West Nile virus, and Japaneseencephalitis virus); and Coronaviruses (examples of which include SARScoronaviruses, such as the Urbani strain). Exemplary negative-strand RNAviruses include, but are not limited to: Orthomyxyoviruses (such as theinfluenza virus), Rhabdoviruses (such as Rabies virus), andParamyxoviruses (examples of which include measles virus, respiratorysyncytial virus, and parainfluenza viruses).

Polioviruses are small (28 nm diameter), non-enveloped viruses whosesingle-stranded genome is enclosed in a capsid of 60 identical subunitsarranged in icosahedral symmetry. Their positive-stranded genomes (˜7500nt) can serve directly as a messenger RNA, which is translated as alarge (˜250 kD) polyprotein from a single ORF. The polyprotein ispost-translationally processed in a proteolytic cascade catalyzed byvirus-encoded proteases, producing at least 10 distinct final cleavageproducts. Polioviruses grow rapidly in a wide variety of cultured humanand simian cells, yielding 10³ to 10⁴ infectious particles per infectedcell in ˜8 hours. As with other RNA viruses, the poliovirus replicaselacks proofreading activity and consequently has a very high rate ofbase misincorporation (˜10⁻⁴ base substitution per base pair perreplication; see Domingo et al. 2002. Error frequencies of picornavirusRNA polymerases: evolutionary implications for virus populations, p.285-298. In B. L. Semler and E. Wimmer (ed.), Molecular Biology ofPicornaviruses. ASM Press, Washington, D.C.; Drake and Holland, Proc.Natl. Acad. Sci. USA 96:13910-13, 1999). Polioviruses exist as threestable serotypes, and for each serotype strains with reduced replicativefitness (the “attenuated” Sabin oral poliovirus vaccine [OPV] strains)have been used throughout the world as live virus vaccines; see Sutteret al., 2003. Poliovirus vaccine—live, p. 651-705. In S. A. Plotkin andW. A. Orenstein (ed.), Vaccines, Fourth ed. W.B. Saunders Company,Philadelphia).

Viruses also include DNA viruses. DNA viruses include, but are notlimited to: Herpesviruses (such as Varicella-zoster virus, for examplethe Oka strain; cytomegalovirus; and Herpes simplex virus (HSV) types 1and 2), Adenoviruses (such as Adenovirus type 1 and Adenovirus type 41),Poxviruses (such as Vaccinia virus), and Parvoviruses (such asParvovirus B19).

Another group of viruses includes Retroviruses. Examples of retrovirusesinclude, but are not limited to: human immunodeficiency virus type 1(HIV-1), such as subtype C, HIV-2; equine infectious anemia virus;feline immunodeficiency virus (FIV); feline leukemia viruses (FeLV);simian immunodeficiency virus (SIV); and avian sarcoma virus.

Another type of pathogen are bacteria. Bacteria can be classified asgram-negative or gram-positive. Exemplary gram-negative bacteriainclude, but are not limited to: Escherichia coli (K-12 and O157:H7),Shigella dysenteriae, and Vibrio cholerae. Exemplary gram-positivebacteria include, but are not limited to: Bacillus anthracis,Staphylococcus aureus, pneumococcus, gonococcus, and streptococcalmeningitis.

Protozoa, nematodes, and fungi are also types of pathogens. Exemplaryprotozoa include, but are not limited to, Plasmodium, Leishmania,Acanthamoeba, Giardia, Entamoeba, Cryptosporidium, Isospora,Balantidium, Trichomonas, Trypanosoma, Naegleria, and Toxoplasma.Exemplary fungi include, but are not limited to, Coccidiodes immitis andBlastomyces dermatitidis. There is a great need for effective vaccinesagainst protozoan pathogens. No effective vaccines for fungal pathogenshave yet been identified.

Exemplary Genes which can be Deoptimized

The gene(s) (for example its corresponding coding sequence) chosen forcodon deoptimization can vary depending on the pathogen of interest. Inone example, one of the coding sequences deoptimized is a single copygene that is important for survival of the pathogen, such as a“housekeeping” gene. In some examples, one of the coding sequencesdeoptimized is a determinant of immunity, such as a viral capsid codingsequence.

In one example, the virus is a positive strand virus, such as apicornavirus, for example a poliovirus, (for example the Sabin type 2OPV strain or the MEF1 reference strain used in the inactivatedpoliovirus vaccine [IPV]) or foot-and-mouth-disease virus (FMDV) (suchas serotype 0), having one or more codons deoptimized in the capsidregion of the virus. In one example, one or more of the Arg codons (suchas all of the Arg codons in a reading frame) are replaced with a rareArg codon, such as CGG. Such CGG-deoptimized picornaviruses can be usedto produce inactivated poliovirus vaccine (IPV) in Vero cells expressingelevated levels of the corresponding rare tRNA. Such CGG-deoptimized IPVseed strains are less likely to infect workers in IPV productionfacilities, enhancing poliovirus containment after global polioeradication.

In one example, the positive strand virus is a togavirus, such as arubella virus or alphavirus. In a particular example, the completegenome of such a virus is de-optimized. However, particular codingsequences can be de-optimized, such as envelope (E) protein E1, E2 orcore protein.

In a specific example, the positive strand virus is a flavivirus, suchas a dengue virus, West Nile virus, or Japanese encephalitis virus, andone or more codons in the coding sequence of a surface glycoprotein genedeoptimized (such as 8 different amino acid codons).

In a specific example, the positive strand virus is a coronavirus, suchas the SARS coronaviruses (for example the Urbani strain). Such virusescan have one or more codons deoptimized in the coding sequence of aspike glycoprotein region (such as at least 5 different amino acidcodons deoptimized).

In one example, the pathogen is an RNA virus, such as a negative-strandRNA virus. In a specific example, the virus is an orthomyxyovirus, suchas an influenza virus (such as strain H3N2), having one or more codonsdeoptimized in a hemagglutinin (HA) or neuraminidase (NA) codingsequence. In one example, the virus is a paramyxovirus, such as ameasles virus having one or more codons deoptimized in a fusion (F) orhemagglutinin (H) coding sequence, or a respiratory syncytial virushaving one or more codons deoptimized in a fusion (F) or glycoprotein(G) coding sequence.

In one example, the pathogen is a retrovirus, such as HIV-1 or HIV-2,and one or more codons are deoptimized in an envelope (env) or groupantigen (gag) coding sequence.

In one example, the pathogen is a DNA virus, such as herpesviruses. In aspecific example, the virus is a varicella zoster virus (such as the Okastrain), and one or more codons are deoptimized in a glycoprotein E or Hcoding sequence. In another specific example, the virus is acytomegalovirus, and one or more codons are deoptimized in aglycoprotein B, H, or N coding sequence. In yet another specificexample, the virus is herpes simplex virus types 1 or 2, and one or morecodons are deoptimized in genes encoding surface glycoprotein B,glycoprotein D, integument protein, or the large subunit ofribonucleotide reductase.

In one example, the pathogen is a bacterium, such as gram-positive orgram-negative bacteria. In one gram-negative example, the bacterium isEscherichia coli (such as strains K-12 or O157:H7), and one or more Argcodons (such as all Arg codons) are replaced with the rare codon AGG inthe ArgS gene (arginyl synthetase gene) and the highly expressed TufAgene (translation factor U). In another example, the bacterium is aShigella dysenteriae, and one or more Arg codons (such as all Argcodons) are replaced with AGG in the RdsB gene. In one gram-positiveexample, the bacterium is Staphylococcus aureus, and one or more Argcodons (such as all Arg codons) are replaced with AGG in the RplB andFusA genes.

Pathogens with Deoptimized Codon Sequences as Immunogenic Compositions

The disclosed attenuated pathogens having a nucleic acid coding sequencewith one or more deoptimized codons can be used in an immunogeniccomposition. In some examples, the deoptimized pathogens are furtherattenuated, for example by passage at suboptimal growth temperatures.Such immunogenic compositions can be used to produce an immune responseagainst the pathogen in a subject, for example to treat a subjectinfected with the pathogen, decrease or inhibit infection by thepathogen, or reduce the incidence of the development of clinicaldisease.

In forming a composition for generating an immune response in a subject,or for vaccinating a subject, a purified, diluted, or concentratedpathogen can be utilized.

Compositions Including a Deoptimized Pathogen

In one example, purified or concentrated (or diluted) deoptimizedpathogens that have one or more codons deoptimized are provided. In someexamples, the immunogenic compositions are composed of non-toxiccomponents, suitable for infants, children of all ages, and adults. Alsodisclosed are methods for the preparation of a vaccine, which includeadmixing a deoptimized pathogen of the disclosure and a pharmaceuticallyacceptable carrier. Although particular examples of deoptimizedsequences are provided herein, one skilled in the art will appreciatethat further modifications to the nucleic acid or protein sequence ofthe pathogen can be made without substantially altering the reducedreplicative fitness due to the deoptimized codons. Examples of suchfurther modifications include one or more deletions, substitutions,insertions, or combinations thereof, in the nucleic acid or proteinsequence. In one example, such further modifications to a deoptimizedpathogenic sequence do not increase the replicative fitness of thedeoptimized pathogenic sequence by more than 5%, such as no more than10%, as compared to an amount of replicative fitness by the deoptimizedpathogen.

In one example, deoptimized pathogen sequences that include additionalamino acid deletions, amino acid replacements, isostereomer (a modifiedamino acid that bears close structural and spatial similarity to theoriginal amino acid) substitutions, isostereomer additions, and aminoacid additions can be utilized, so long as the modified sequences do notincrease the replicative fitness of the deoptimized pathogenic sequenceby more than 5%, and retain the ability to stimulate an immune responseagainst the pathogen. In another example, deoptimized pathogen sequencesthat include nucleic acid deletions, nucleic acid replacements, andnucleic acid additions can be utilized, so long as the modifiedsequences do not increase the replicative fitness of the deoptimizedpathogenic sequence by more than 5%, and retains the ability tostimulate an immune response against the pathogen.

In one example, the deoptimized pathogenic nucleic acid sequences arerecombinant.

The deoptimized pathogens can be replicated by methods known in the art.For example, pathogens can be transferred into a suitable host cell,thereby allowing the pathogen to replicate. The cell can be prokaryoticor eukaryotic.

The disclosed deoptimized pathogens can be used as immunogeniccompositions, such as a vaccine. In one example, an immunogeniccomposition includes an immunogenically effective amount (or therapeuticamount) of an attenuated deoptimized pathogen of the disclosure, such asa viral, bacterial, fungal, or protozoan deoptimized pathogen.Immunogenically effective refers to the amount of attenuated deoptimizedpathogen (live or inactive) administered at vaccination sufficient toinduce in the host an effective immune response against virulent formsof the pathogen. An effective amount can being readily determined by oneskilled in the art, for example using routine trials establishing doseresponse curves. In one example, the deoptimized pathogen can range fromabout 1% to about 95% (w/w) of the composition, such as at least 10%, atleast 50%, at least 75%, or at least 90% of the composition.

Pharmaceutical compositions that include a deoptimized pathogen can alsoinclude other agents, such as one or more pharmaceutically acceptablecarriers or other therapeutic ingredients (for example, antibiotics). Inone example, a composition including an immunogenically effective amountof attenuated deoptimized pathogen also includes a pharmaceuticallyacceptable carrier. Particular examples of pharmaceutically acceptablecarriers include, but are not limited to, water, culture fluid in whichthe pathogen was cultured, physiological saline, proteins such asalbumin or casein, and protein containing agents such as serum. Otheragents that can be included in the disclosed pharmaceuticalcompositions, such as vaccines, include, but are not limited to, pHcontrol agents (such as arginine, sodium hydroxide, glycine,hydrochloric acid, citric acid, and the like), local anesthetics (forexample, benzyl alcohol), isotonizing agents (for example, sodiumchloride, mannitol, sorbitol), adsorption inhibitors (for example, Tween80), solubility enhancing agents (for example, cyclodextrins andderivatives thereof), stabilizers (for example, serum albumin, magnesiumchloride, and carbohydrates such as sorbitol, mannitol, starch, sucrose,glucose, and dextran), emulsifiers, preservatives, (such aschlorobutanol and benzalkonium chloride), wetting agents, and reducingagents (for example, glutathione).

When the immunogenic composition is a liquid, the tonicity of theformulation, as measured with reference to the tonicity of 0.9% (w/v)physiological saline solution taken as unity, can be adjusted to a valueat which no substantial, irreversible tissue damage will be induced atthe site of administration. Generally, the tonicity of the solution isadjusted to a value of about 0.3 to about 3.0, such as about 0.5 toabout 2.0, or about 0.8 to about 1.7.

DNA Immunogenic Compositions

In one example, an immunogenic composition includes a deoptimizednucleic acid coding sequence instead of (or in addition to) the entiredeoptimized pathogen. In particular examples, the sequence includes asequence having at least 90%, at least 95%, or 100% sequence identity toany of SEQ ID NOS: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45,48, 51, 54, 55, 56, 57, 58, 67, 68, or 69. In some examples, animmunogenic composition includes a full-length deoptimized genome, forexample a deoptimized poliovirus genome. However, one skilled in the artwill appreciate that fragments of the deoptimized full-length genome canalso be used (and in some examples ligated together). The DNA includingthe deoptimized coding sequence can be part of a vector, such as aplasmid, which is administered to the subject. Such DNA immunogeniccompositions can be used to stimulate an immune response using themethods disclosed herein.

In one example, a deoptimized nucleic acid coding sequence from apathogen is present in a colloidal dispersion system. Colloidaldispersion systems include macromolecule complexes, nanocapsules,microspheres, beads, and lipid-based systems including oil-in-wateremulsions, micelles, mixed micelles, and liposomes. Large uni-lamellarvesicles (LUV), which range in size from 0.2-4.0 μm can encapsulate asubstantial percentage of an aqueous buffer containing largemacromolecules. RNA, DNA and intact virions can be encapsulated withinthe aqueous interior and be delivered to cells in a biologically activeform (Fraley et al., Trends Biochem. Sci. 6:77, 1981).

The composition of a liposome is usually a combination of phospholipids,particularly high-phase-transition-temperature phospholipids, usually incombination with steroids, such as cholesterol. Examples of lipidsuseful in liposome production include phosphatidyl compounds, such asphosphatidylglycerol, phosphatidylcholine, phosphatidylserine,phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides.Particularly useful are diacylphosphatidyl-glycerols, where the lipidmoiety contains from 14-18 carbon atoms, such as 16-18 carbon atoms, andis saturated. Illustrative phospholipids include eggphosphatidylcholine, dipalmitoylphosphatidylcholine anddistearoylphosphatidylcholine.

Inducing an Immune Response

Methods are disclosed for stimulating an immune response in a subjectusing the disclosed deoptimized pathogens (such as a pathogen thatincludes a sequence having at least 90%, at least 95% or 100% sequenceidentity to any of SEQ ID NOS: 5, 8, 11, 14, 18, 21, 24, 27, 30, 33, 36,39, 42, 45, 48, 51, 54, 55, 56, 57, 58, 67, 68, or 69) and immunogeniccompositions. The method includes administering to a subject animmunologically effective amount of a deoptimized pathogen having anucleic acid coding sequence with one or more deoptimized codons, whichreduce the replicative fitness of the pathogen (for example by at least20%, at least 50%, or even at least 99%). Such administration can bebroadly effective for treatment and prevention of disease caused by apathogen, and one or more associated symptoms thereof. In one example,the immunogenic compositions and methods are designed to confer specificimmunity against infection with a pathogen, and to induce antibodiesspecific to the pathogen. The deoptimized pathogens can be delivered toa subject in a manner consistent with conventional methodologiesassociated with management of the disorder for which treatment orprevention is sought.

In selected examples, one or more symptoms or associated effects ofexposure to or infection with a pathogen is prevented or treated byadministration to a subject at risk of being infected by the pathogen,or presenting with one or more symptoms associated with infection by thepathogen, of an effective amount of a deoptimized pathogen of thedisclosure. Therapeutic compositions and methods of the disclosure forprevention or treatment of toxic or lethal effects of pathogen infectionare applicable to a wide spectrum of infectious agents.

Administration of Deoptimized Pathogens

For administration to animals or humans, the immunogenic compositions ofthe present disclosure, including vaccines, can be given by any methoddetermined appropriate by a clinician. In addition, the immunogeniccompositions disclosed herein can be administered locally orsystemically. Types of administration include, but are not limited to,intramuscular, subcutaneous, oral, intravenous, intra-atrial,intra-articular, intraperitoneal, parenteral, intraocular, and by avariety of mucosal administration modes, including by oral, rectal,intranasal, intrapulmonary, or transdermal delivery, or by topicaldelivery to other surfaces.

The disclosed methods include administering a therapeutically effectiveamount of an attenuated pathogen having one or more deoptimized codonsequences (a deoptimized pathogen) to generate an immune responseagainst the pathogen. Specific, non-limiting examples of an immuneresponse are a B cell or a T cell response. Upon administration of thedeoptimized pathogen, the immune system of the subject responds to theimmunogenic composition (such as a vaccine) by producing antibodies,both secretory and serum, specific for one or more pathogen epitopes.Such a response signifies that an immunologically effective dose of thedeoptimized pathogen was delivered. An immunologically effective dosagecan be achieved by single or multiple administrations. In some examples,as a result of the vaccination, the subject becomes at least partiallyor completely immune to infection by the pathogen, resistant todeveloping moderate or severe pathogen infection, or protected fromdisease associated with infection by the pathogen. For example, aneffective dose can be measured by detection of a protective antibodytiter in the subject.

Typical subjects that can be treated with the compositions and methodsof the present disclosure include humans, as well as veterinary subjectssuch as dogs, cats, horses, chickens, cows, fish, sheep, and pigs. Toidentify subjects for treatment according to the methods of thedisclosure, accepted screening methods can be employed to determine riskfactors associated with a targeted or suspected disease of condition(for example, polio) as discussed herein, or to determine the status ofan existing disease or condition in a subject. These screening methodsinclude, for example, conventional work-ups to determine environmental,familial, occupational, and other such risk factors that may beassociated with the targeted or suspected disease or condition, as wellas diagnostic methods, such as various ELISA and other immunoassaymethods, which are available and well known in the art to detect orcharacterize disease-associated markers, such as antibodies present inthe serum of a subject indicating that they were previously infectedwith a particular pathogen. The vaccines can also be administered aspart of a routine health maintenance program in at risk individuals,such as the administration of meningococcal vaccines in children andpneumococcal or influenza vaccines in the elderly. These and otherroutine methods allow a clinician to select subjects in need of therapyusing the methods and pharmaceutical compositions of the disclosure. Inaccordance with these methods and principles, a deoptimized pathogen canbe administered using the methods disclosed herein as an independentprophylaxis or treatment program, or as a follow-up, adjunct orcoordinate treatment regimen to other treatments, such as surgery,vaccination, or immunotherapy.

The compositions including deoptimized pathogens can be used fortherapeutic purposes, such as prophylactically. When providedprophylactically, deoptimized pathogens are provided in advance of anysymptom associated with the pathogen against which the prophylaxis isprovided. The prophylactic administration of deoptimized pathogensserves to prevent or ameliorate any subsequent infection. When providedtherapeutically, deoptimized pathogens are provided at (or shortlyafter) the onset of a symptom of disease or infection. The discloseddeoptimized pathogens can thus be provided prior to the anticipatedexposure to a particular pathogen, so as to attenuate the anticipatedseverity, duration or extent of an infection or associated diseasesymptoms, after exposure or suspected exposure to the pathogen, or afterthe actual initiation of an infection.

The deoptimized pathogens disclosed herein can be administered to thesubject in a single bolus delivery, via continuous delivery (forexample, continuous transdermal, mucosal, or intravenous delivery) overan extended time period, or in a repeated administration protocol (forexample, by an hourly, daily, weekly, or monthly repeated administrationprotocol). In one example, administration of a daily dose can be carriedout both by single administration in the form of an individual dose unitor else several smaller dose units and also by multiple administrationsof subdivided doses at specific intervals.

The therapeutically effective dosage of a deoptimized pathogen can beprovided as repeated doses within a prolonged prophylaxis or treatmentregimen that will yield clinically significant results to alleviate oneor more symptoms or detectable conditions associated with a targeteddisease or condition as set forth herein. Determination of effectivedosages are typically based on animal model studies followed up by humanclinical trials and is guided by administration protocols thatsignificantly reduce the occurrence or severity of targeted diseasesymptoms or conditions in the subject. Various considerations aredescribed, e.g., in Gilman et al., eds., Goodman and Gilman: ThePharmacological Bases of Therapeutics, 8th ed., Pergamon Press, 1990;and Remington's Pharmaceutical Sciences, 17^(th) ed., Mack PublishingCo., Easton, Pa., 1990, each of which is herein incorporated byreference. Suitable models in this regard include, for example, murine,rat, porcine, feline, non-human primate, and other accepted animal modelsubjects known in the art.

Immunologically effective dosages can also be determined using in vitromodels (for example, immunologic and histopathologic assays). Using suchmodels, only ordinary calculations and adjustments are used to determinean appropriate concentration and dose to administer a therapeuticallyeffective amount of the deoptimized pathogen (for example, amounts thatare effective to elicit a desired immune response or alleviate one ormore symptoms of a targeted disease). In some examples, amountsadministered are those amounts adequate to achieve tissue concentrationsat the site of action which have been found to achieve the desiredeffect in vitro. In alternative examples, an effective amount oreffective dose of the deoptimized pathogens can decrease or enhance oneor more selected biological activities correlated with a disease orcondition.

For example, deoptimized pathogens of the present application can betested using in vitro and in vivo models to confirm adequateattenuation, genetic stability, and immunogenicity for vaccine use. In aparticular example, an in vitro assay is used to determine theattenuation and genetic stability of a deoptimized pathogen, for exampleusing the plaque assays and virus yield, single-step growth assaysdescribed herein. In another example, deoptimized pathogens are furthertested in animal models of infection, for example using the methodsdescribed herein. For example, a deoptimized pathogen can beadministered to an animal model, and an amount of immunogenic responseto the deoptimized pathogen determined, for example by analyzingantibody, T-cell or B-cell production. In some examples, the animal isfurther exposed to the pathogen, and resistance to infection determined.

The actual dosage of the deoptimized pathogen can vary according tofactors such as the disease indication and particular status of thesubject (for example, the subject's age, weight, fitness, extent ofsymptoms, susceptibility factors, and the like), time and route ofadministration, the type of pathogen against which vaccination issought, other drugs or treatments being administered concurrently, aswell as the specific pharmacology of the deoptimized pathogens foreliciting the desired activity or biological response in the subject.Dosage regimens can be adjusted to provide an optimum prophylactic ortherapeutic response. A therapeutically effective amount is also one inwhich any toxic or detrimental side effects of a deoptimized pathogenare outweighed in clinical terms by therapeutically beneficial effects.

In one example, an immunogenic composition includes any dose ofdeoptimized bacteria sufficient to evoke an immune response, such as arange of between 10³ and 10¹⁰ bacteria per dose, for example at least10³ bacteria, at least 10⁴ bacteria, at least 10⁵ bacteria, at least 10⁸bacteria, or at least 10⁹ bacteria per dose. In one example, animmunogenic composition includes any dose of deoptimized virionssufficient to evoke an immune response, such as a range of between 10³to 10¹⁰ plaque forming units (PFU) or more of virus per subject, such as10⁴ to 10⁵ PFU virus per subject, for example at least 10³ PFU virus persubject, at least 10⁴ PFU virus per subject, at least 10⁵ PFU virus persubject, or at least 10⁹ PFU virus per subject. In another example, animmunogenic composition includes any dose of deoptimized protozoasufficient to evoke an immune response, such as at least 10² infectiousunits per subject, for example at least 10³ infectious units persubject, or a range of between 10² to 10⁶ infectious units per subject.In any event, the immunogenic compositions ideally provide a quantity ofdeoptimized pathogen sufficient to effectively protect the subjectagainst serious or life-threatening pathogen infection.

For each particular subject, specific dosage regimens can be evaluatedand adjusted over time according to the individual need and professionaljudgment of the person administering or supervising the administrationof the deoptimized pathogen. For example, in neonates and infants,multiple administrations can be required to elicit sufficient levels ofimmunity. In some examples, administration of the disclosed immunogeniccompositions begins within the first month of life and continues atintervals throughout childhood, such as at two months, six months, oneyear and two years, as necessary to maintain sufficient levels ofprotection against pathogen infection. Similarly, adults who areparticularly susceptible to repeated or serious infection by pathogens,such as health care workers, day care workers, elderly individuals, andindividuals with compromised cardiopulmonary function, may requiremultiple immunizations to establish or maintain protective immuneresponses. Levels of induced immunity can be monitored by measuringamounts of neutralizing secretory and serum antibodies, and dosagesadjusted or vaccinations repeated as necessary to maintain desiredlevels of protection.

The antibody response of a subject administered the compositions of thedisclosure can be determined by using effective dosages/immunizationprotocols. In some examples, it is sufficient to assess the antibodytiter in serum or plasma obtained from the subject. Decisions as towhether to administer booster inoculations or to change the amount ofthe immunogenic composition administered to the individual can be atleast partially based on the antibody titer level. The antibody titerlevel can be based on, for example, an immunobinding assay whichmeasures the concentration of antibodies in the serum which bind to aspecific antigen present in the pathogen. The ability to neutralize invitro and in vivo biological effects of the pathogen of interest canalso be assessed to determine the effectiveness of the treatment.

Dosage can be varied by the attending clinician to maintain a desiredconcentration at a target site. Higher or lower concentrations can beselected based on the mode of delivery. Dosage can also be adjustedbased on the release rate of the administered formulation. To achievethe same serum concentration level, for example, slow-release particleswith a release rate of 5 nanomolar (under standard conditions) would beadministered at about twice the dosage of particles with a release rateof 10 nanomolar.

Kits

The instant disclosure also includes kits, packages and multi-containerunits containing the herein described deoptimized pathogens, alone or inthe presence of a pharmaceutically acceptable carrier, and in someexamples, an adjuvant. Such kits can be used in the treatment ofpathogenic diseases in subjects. In one example, these kits include acontainer or formulation that contains one or more of the deoptimizedpathogens described herein. In one example, this component is formulatedin a pharmaceutical preparation for delivery to a subject. Thedeoptimized pathogens can be contained in a bulk dispensing container orunit or multi-unit dosage form.

Optional dispensing means can be provided, for example a pulmonary orintranasal spray applicator, or a needle. Packaging materials optionallyinclude a label or instruction indicating for what treatment purposes,or in what manner the pharmaceutical agent packaged therewith can beused.

The subject matter of the present disclosure is further illustrated bythe following non-limiting Examples.

Example 1 Codon Usage in Poliovirus

This example describes methods used to determine codon usage inpoliovirus.

Mononucleotide and dinucleotides frequencies, and codon usage wereanalyzed in the original reports of poliovirus genomic sequences(Kitamura et al. 1981. Nature 291:547-53; Racaniello and Baltimore.1981. Proc. Natl. Acad. Sci. USA 78:4887-91; Rothberg and Wimmer. 1981.Nucleic Acids Res. 9:6221-9; Toyoda et al. 1984. J. Mol. Biol.174:561-85). The mono-, di-, and trinucleotide frequency patterns aresimilar for the three Sabin strains (Toyoda et al. 1984. J. Mol. Biol.174:561-85) and appear to be conserved across poliovirus genotypes(Hughes et al. 1986. J. Gen. Virol. 67:2093-102; Kew et al. 2002.Science 296:356-9; La Monica et al. 1986. J. Virol. 57:515-25; Liu etal. 2003. J. Virol. 77:10994-1005; Martin et al. 2000. Virology278:42-9; Yang et al. 2003. J. Virol. 77:8366-77) and human enterovirusspecies C serotypes (Brown et al. 2003. J. Virol. 77:8973-84).

As with other enteroviruses, the component bases in the Sabin 2 ORF arepresent in approximately equal proportions (24.0% U, 22.9% C, 29.9% A,and 23.1% G; see Rezapkin et al., Virology 258:152-60, 1999; Toyoda etal., J. Mol. Biol. 174:561-85, 1984), thus permitting a low bias incodon usage (Osawa et al., Microbiol. Rev. 56:229-264, 1992). Indeed,all codons are used in poliovirus ORFs (Toyoda et al., J. Mol. Biol.174:561-85, 1984), and the overall degree of codon usage bias is low(Jenkins and Holmes. Virus Res. 92:1-7, 2003).

One measure of codon usage bias is the number of effective codons(N_(C)), which can vary from 20 (only one codon used for each aminoacid) to 61 (all codons used randomly) (Wright, Gene 87:23-9, 1990). TheN_(C) values for Sabin 2 are 56.0 for the capsid region and 54.6 for thecomplete ORF. As with the genomes of vertebrates and most RNA viruses,the dinucleotide CG is suppressed in the Sabin 2 genome (Toyoda et al.,J. Mol. Biol. 174:561-85, 1984), and the observed pattern of codon usagereflects this CG suppression (Table 1).

TABLE 1 Codon usage in mutagenized capsid interval and complete ORF inunmodified and deoptimized Sabin 2 genomes. Codon usage (number) Capsidinterval Complete ORF (nt 748 to 3303) (nt 748 to7368) Amino ConstructConstruct acid Codon^(a) ABCD^(b) ABCd^(c) abcd^(d) ABCD ABCd abcd ArgCGA 4 1 0 7 4 3 CGC 11 7 0 13 9 2 CGG 2 17 39 7 22 44 CGU 0 0 0 3 3 3AGA 17 9 0 45 37 28 AGG 5 5 0 23 23 18 Leu CUA 7 6 1 33 32 27 CUC 7 6 027 26 20 CUG 14 10 0 25 21 11 CUU 4 14 55 22 32 73 UUA 9 9 1 25 25 17UUG 18 14 2 40 36 24 Ser UCA 18 11 0 43 36 25 UCC 14 11 2 33 30 21 UCG 61 0 8 3 2 UCU 8 7 0 19 18 11 AGC 9 25 63 20 36 74 AGU 10 10 0 26 26 16Thr ACA 20 17 0 47 44 27 ACC 24 19 1 55 50 32 ACG 11 23 74 17 29 80 ACU20 16 0 47 43 27 Pro CCA 21 16 0 53 48 32 CCC 19 15 0 32 28 13 CCG 9 2159 19 31 69 CCU 12 9 2 18 15 8 Ala GCA 23 16 0 61 54 38 GCC 16 13 2 4037 26 GCG 10 26 66 17 33 73 GCU 19 13 0 49 43 30 Gly GGA 12 8 0 38 34 26GGC 8 7 0 30 29 22 GGG 20 16 2 37 33 19 GGU 14 23 52 42 51 80 Val GUA 108 1 24 22 15 GUC 10 27 55 21 38 66 GUG 20 10 1 55 45 36 GUU 17 12 0 4035 23 Ile AUA 16 12 0 30 26 14 AUC 15 22 45 47 54 77 AUU 14 11 0 59 5645 Lys AAA 13 13 13 64 64 64 AAG 18 18 18 58 58 58 Asn AAC 25 25 25 6161 61 AAU 25 25 25 52 52 52 Gln CAA 18 18 18 47 47 47 CAG 9 9 9 32 32 32His CAC 12 12 12 30 30 30 CAT 6 6 6 19 19 19 Glu GAA 16 16 16 57 57 57GAG 19 19 19 56 56 56 Asp GAC 23 23 23 51 51 51 GAU 19 19 19 62 62 62Tyr UAC 21 21 21 57 57 57 UAU 16 16 16 43 43 43 Cys UGC 10 10 10 20 2020 UGU 5 5 5 22 22 22 Phe UUC 14 14 14 36 36 36 UUU 21 21 21 48 48 48Met AUG 26 26 26 67 67 67 Trp UGG 13 13 13 28 28 28 ^(a)Unpreferredcodons used as replacement codons are shown in boldface font. ^(b)ABCDrepresents virus construct S2R9, which differs from the reference Sabin2 strain sequence at three synonymous third-position sites: A₂₆₁₆ → G(VP1 region), A₃₃₀₃ → T (VP1 region), and T₅₆₄₀ → A (3C^(pro) region).^(c)ABCd represents virus construct S2R19, which has replacement codonsacross an interval spanning 76% of the VP1 region. ^(d)abcd representsvirus construct S2R23, which has replacement codons across an intervalspanning 97% of the capsid region.

Example 2 Poliovirus Containing a Deoptimized Capsid Region

This example describes methods used to generate a poliovirus containingdeoptimized codons in the capsid region. Briefly, the original capsidregion codons of the Sabin type 2 oral polio vaccine strain werereplaced with synonymous codons less frequently used in poliovirusgenomes. An unpreferred synonymous codon was used nearly exclusively tocode for each of nine amino acids. Codon changes were introduced intofour contiguous intervals spanning 97% of the capsid region.

The strategy for codon replacement was as follows. Despite the lowoverall bias in codon usage in Sabin 2, some synonymous codons are usedat much lower frequencies than others (Table 1). To determine codonusage in Sabin 2, the preferred codons for each of nine amino acids werereplaced with a synonymous unpreferred codon (Table 1). The codonreplacements shown in Table 1 were introduced only within the capsidsequences, because those sequences uniquely identify a poliovirusserotype, as both noncapsid and 5′-UTR region sequences are exchangedout by recombination with other species C enteroviruses duringpoliovirus circulation.

Because codon usage bias was very low for most two-fold degeneratecodons (except codons for His and Tyr), only six-fold, four-fold, andthree-fold degenerate codons were replaced. Synonymous codons for nineamino acids were replaced by a single unpreferred codon: CUU for Leu,AGC for Ser, CGG for Arg, CCG for Pro, GUC for Val, ACG for Thr, GCG forAla, GGU for Gly, and AUC for Ile (Table 1). Whenever possible, codonswith G or C at degenerate positions (the nucleotides that differ withinthe codons that encode for a particular amino acid) were chosen toincrease the G+C content of the modified viral genomes.

For example, as shown in Table 1, the amino acid Leu is encoded by 6different codons in Sabin 2. However, the codon CUU is used the leastfrequently of the six. Therefore, it was selected to replace the otherfive codons. Similarly, the amino acid Pro is encoded by four differentcodons in Sabin 2. However, the codon CCG is used the least frequentlyof the four. Therefore, it was selected to replace the other threecodons. A similar analysis was performed for the least frequently usedcodon for Thr and Ala. For the amino acid Ser, although the codon UCGwas less frequently used than AGC in Sabin 2, AGC was chosen todeoptimize the sequence because it was the least preferred Ser codonamong a larger collection of VP1 sequences of wild polioviruses.Similarly, GGU was the least preferred Gly codon among a largercollection of VP1 sequences of wild polioviruses. Codons CGG and AUCwere selected for Arg and Ile, respectively, because they were notpreferred and their usage would increase the G+C content of thepoliovirus genome.

In addition, some codons did not display a significant amount of bias,and were therefore not selected. For example, the amino acid Asp isencoded in the Sabin 2 capsid region by 19 and 23 GAU and GAC codons,respectively. Similarly, the amino acid Glu is encoded in the Sabin 2capsid region by 16 and 19 GAA and GAG codons, respectively. Since thesevalues are similar, it is not likely that substitution of one for theother would reduce replicative fitness of the pathogen. Ideally, in thecase where there are at least two codons that encode for an amino acidin the pathogen, there is at least a 20% difference between the selectedcodon and one or more of the other codons that encode the amino acid,such as an at least 30% difference, or an at least 50% difference.

Replacement codons were introduced into a full-length infectious cDNAclone derived from Sabin 2 (construct S2R9) within an interval (nt 748to 3302) spanning all but the last 27 codons of the capsid region (FIGS.1A-D). The capsid interval was divided into four mutagenesis cassettes:A (nt 657 to 1317; 661 bp), B (nt 1318 to 2102; 785 bp), C (nt 2103 to2615; 513 bp), and D (nt 2616 to 3302; 687 bp) (FIG. 1A). Mutagenesiscassette A, bounded by restriction sites BstZ17I and AvrII, includes thelast 91 nucleotides of the 5′-UTR, but no 5′-UTR sequences were modifiedin cassette A. Within each cassette, synonymous codons for the nineamino acids were comprehensively replaced except at 15 positions(replacement at 11 of these positions would have eliminated desirablerestriction sites or generated undesirable restriction sites).Unmodified cassettes are identified by uppercase italic letters; thecorresponding cassettes with replacement codons are identified bylowercase italic letters. Thus, as shown in FIG. 2, the reference Sabin2 derivative (derived from cDNA construct S2R9) is identified as ABCD(SEQ ID NO: 3), and the fully modified virus (derived from cDNAconstruct S2R23) is identified as abcd (SEQ ID NO: 5).

The methods described below were used to generate the deoptimizedpolioviruses.

Virus and Cells.

The Sabin Original+2 (Sabin and Boulger. J. Biol. Stand. 1:115-8, 1973)master seed of the Sabin type 2 oral poliovaccine strain (P712 ch tab)was provided by R. Mauler of Behringwerke AG (Marburg, Germany). Viruswas grown at 35° C. in suspension cultures as previously described(Rueckert and Pallansch. Meth. Enzymol. 78:315-25, 1981) of S3 HeLacells (human cervical carcinoma cells; ATCC CCL-2.2) or in monolayercultures of HeLa (ATCC CCL-2), and RD (human rhabdomyosarcoma cells;ATCC CCL-136) cells. Some initial plaque assays were performed in HEp-2Ccells (Chen, Cytogenet. Cell Genet. 48:19-24, 1988).

Preparation of Infectious Sabin 2 Clones.

Poliovirus RNA was extracted from 250 μl of cell culture lysate (from˜75,000 infected cells) by using TRIZOL LS reagent (Life Technologies,Rockville, Md.) and further purified on CENTRI-SEP columns (PrincetonSeparations, Adelphia, N.J.). Full-length cDNA was reversed transcribed(42° C. for 2 hours) from ˜1 μg of viral RNA in a 20 μl reactioncontaining 500 μM dNTP (Roche Applied Science, Indianapolis, Ind.), 200U Superscript II Reverse Transcriptase (Life Technologies), 40 URNase-inhibitor (Roche), 10 mM dithiothreitol, and 500 ng primer52-7439A-B [CCTAAGC(T)₃₀CCCCGAATTAAAGAAAAATTTACCCCTACA; SEQ ID NO: 1] inSuperscript II buffer.

After reverse transcription, 2 U RNase H (Roche) was added and incubatedat 37° C. for 40 min. Long PCR amplification of viral cDNA was performedusing TaqPlus Precision (Stratagene, La Jolla, Calif.) and AmpliWax PCRGem 100 beads (Applied Biosystems, Foster City, Calif.) for “hot start”PCR in thin-walled tubes. The bottom mix (50 μl) contained 200 μM eachdNTP (Roche) and 250 ng each of primers S2-7439A-B and S2-1S-C(GTAGTCGACTAATACGACTCACTATAGGTTAAAACAGCTCTGGGGTTG; SEQ ID NO: 2) inTaqPlus Precision buffer. A wax bead was added to each tube, and sampleswere heated at 75° C. for 4 minutes and cooled to room temperature. Thetop mix (50 μl) contained 2 μl of the cDNA and 10 U TaqPlus Precision inTaqPlus Precision buffer. The samples were incubated in a thermal cyclerat 94° C. for 1 minute and then amplified by 30 PCR cycles (94° C. for30 seconds, 60° C. for 30 seconds, and 72° C. for 8 minutes), followedby a final 94° C. for 1 minute and final extension of 72° C. for 20minutes.

PCR products were purified using QIAquick PCR purification kit (Qiagen,Valencia, Calif.) and sequentially digested for 2 hours at 37° C. withSal I and Hind III prior to gel purification. PCR products were ligatedto pUC19 plasmids following standard methods (Sambrook and Russell.2001. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y.) and ligated plasmids weretransformed into XL-10 Gold supercompetent E. coli cells (Stratagene).Colonies were screened for recombinant plasmids on X-gal indicatorplates (Sambrook and Russell. 2001. Molecular Cloning: A LaboratoryManual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y.) and 6 white colonies were transferred to 1.5 ml Luria-Bertanibroth containing 50 μg/ml ampicillin (LB/amp) (Roche). Plasmids werepurified using QIAprep Spin Miniprep columns and sequences of theinserts were determined by cycle sequencing using an automated DNAsequencer (Applied Biosystems, Foster City, Calif.) (Liu et al., J.Virol. 74:11153-61, 2000). The full-length viral insert was sequenced inboth orientations using overlapping sense and antisense primers spaced˜500 nt apart. Selected clones were grown in 50 ml LB/amp, andrecombinant plasmids were purified using the QlAfilter Plasmid Maxi kit.

Virus Preparation.

Plasmids were linearized with Hind III and purified using QIAquickcolumns prior to RNA transcription from 1 μg of plasmid DNA using theMegascript T7 In Vitro Transcription kit (Ambion, Austin, Tex.). RNAyields were estimated using DNA Dipsticks (Invitrogen, Carlsbad, Calif.)and RNA chain length was analyzed by electrophoresis on 1% formaldehydegels prior to transfection. RD cells were transfected with transcriptsof viral RNA by using Tfx-20 (Promega, Madison, Wis.). Briefly,semi-confluent RD cells in 12-well cell culture plates were inoculatedwith 500 μl MEM (MEM incomplete) (Life Technologies) containing 0.1 μgviral RNA transcript and 0.45 μl Tfx-20 Reagent. Plates were incubatedfor 1 hour at 35° C. prior to addition of 1.5 ml MEM complete [MEMincomplete supplemented with 100 U penicillin and 100 μg streptomycin, 2mM L-glutamine, 0.075% NaHCO₃, 10 μM HEPES (pH 7.5)] (Life Technologies)containing 3% fetal calf serum (FCS; HyClone, Logan, Utah). Negativecontrols were performed using RNA transcribed from pBluescriptIISK+(Stratagene) containing a viral insert truncated at base 7200 bydigestion with BamHI and transcribed in a reverse orientation from a T3promoter.

Complete CPE was observed after incubation at 35° C. for 18-20 hours atwhich time 400 μl from the transfected wells were transferred to aconfluent RD cell monolayer in 75 cm² flasks containing MEM complete.Complete CPE was observed in the second passage after 24 hours at 35°C., and virus was liberated from the infected cells by three freeze-thawcycles and clarification by centrifugation for 15 minutes at 15,000×g.Control wells were passaged once and monitored for 72 hourspost-transfection. The sequences of all virus stocks were verified byRT-PCR amplification of two large overlapping fragments and subsequentsequence analysis of the PCR product.

Site-Directed Mutagenesis.

Single-base substitutions were introduced using the QuikChangeSite-Directed Mutagenesis Kit (Stratagene). Briefly, two complementaryprimers containing the desired mutation were designed for PCRamplification of the plasmid containing the Sabin 2 insert.Amplification was performed using Pfu Turbo DNA polymerase on 5 ng oftemplate DNA for 15 cycles at 95° C. for 30 s, 50° C. for 1 minute, and68° C. for 23 minutes. PCR products were digested for 1 hour at 37° C.with 10 U of Dpn I prior to transformation in XL-1 Blue Supercompetentcells. Colonies were grown and screened by sequencing as describedabove.

Assembly PCR. Multiple base substitutions were introduced by assemblyPCR using previously described methods (Stemmer et al., Gene 164:49-53,1995). Briefly, primers were designed to span the region of interestwith complementary 40-mers overlapping by 10 nt on each end. A firstround of assembly (30 PCR cycles of 94° C. for 45 seconds, 52° C. for 45seconds, and 72° C. for 45 seconds) was performed with a 20 μl reactionmixture containing Taq Plus Precision buffer, 10 U Taq Plus Precision, 5pmoles of each primer, and 200 μM dNTP. A second round of assembly (25PCR cycles of 94° C. for 45 seconds, 50° C. for 45 seconds, and 72° C.for 2 minutes) was performed using the outermost sense and antisenseprimers in a 100 μl reaction mixture in Taq Plus Precision buffercontaining 2 μl of product from the first assembly round, 10 U Taq PlusPrecision, 200 ng of each primer, and 400 μM dNTP. PCR products werecolumn purified prior to digestion, ligation, and transformation intoXL-10 gold supercompetent E. coli cells. Clones were grown and screenedby sequencing of insert as described.

Construction of Recombinant Clones.

The sequence of the full-length Sabin 2 infectious clone, S2R9, differedfrom the published sequence of a reference Sabin 2 strain (Rezapkin etal., Virology 258:152-60, 1999) at three synonymous third-codonpositions: G₂₆₁₆ (in VP1 region; A replaced to introduce an Eaglrestriction site) T3303 (in VP1 region; A replaced to introduce a XhoIsite), A₅₆₄₀ (in 3C^(pro) region). The S2R9 construct was used as thereference Sabin 2 strain. Recombinant clones having differentcombinations of blocks of replacement codons were constructed usingstandard methods (Kohara et al., J. Virol. 53:786-92, 1985).

As shown in Tables 1 and 2, the modifications introduced dramaticallyaltered the mono-, di-, and trinucleotide (codon) frequencies in thecapsid region. In the fully modified construct, abcd, nearly half(427/879; 48.6%) of the capsid region codons were replaced, and a totalof 544 substitutions (90 first codon position, 44 second position, and410 third position) were introduced into the 2555 mutagenized capsidregion nucleotides. This strategy for codon deoptimization increased thenumber of CG dinucleotides in the poliovirus templates. CG was the leastabundant dinucleotide (181 occurrences) in the unmodified ABCD constructand the most abundant dinucleotide (386 occurrences) in the highlymodified abcd construct. Compared with ABCD, the N_(C) values in thecapsid region of abcd fell from 56.2 to 29.8, the number of CGdinucleotides rose from 97 to 302, and the % G+C increased from 48.4% to56.4% (Table 2). These changes were nearly uniformly distributed overthe mutagenized capsid region (Table 2).

TABLE 2 Effective number of codons used (N_(C)), number of CGdinucleotides, and G + C content in mutagenized capsid region sequences.Length No. of CG of codon N_(C) ^(b) dinucleotides^(c) % G + C replace-Replace- Replace- Replace- ment ment Complete ment Complete mentComplete interval interval capsid Complete interval capsid Completeinterval capsid Complete Construct^(a) (bp) orig/mod^(d) region^(e) ORForig/mod region ORF orig/mod region ORF ABCD ^(f) 2555^(g) 56.0/56.056.2 54.6 94/94 97 181 48.5/48.5 48.4 46.0 aBCD  570^(g) 57.3/30.8 56.156.4 20/63 140 224 48.1/56.0 50.1 46.7 AbCD 785 56.0/29.9 53.1 55.725/89 161 245 48.4/56.1 50.7 47.0 ABcD 513 57.7/28.2 56.3 56.0 13/59 143227 48.3/57.0 50.1 46.7 ABCd 687 54.0/28.4 54.6 56.5 36/88 149 23349.1/57.7 50.7 46.5 abcd 2555  56.0/29.3 29.8 47.3  94/299 302 38648.5/56.7 56.4 49.2 ^(a)Constructs correspond to the followinginfectious cDNA plasmids, clones, and virus derivatives: ABCD, S2R9;aBCD, S2R28; AbCD, not constructed; ABcD, S2R20; ABCd, S2R19; abcd,S2R23; N_(C), number of CG dinucleotides, and % G + C of all otherconstructs can be calculated from table. ^(b)N_(C): effective number ofcodons used (1); one replacement codon spanned the EagI restrictioncleavage site and was counted as part of cassette D. ^(c)One CGdinucleotide spanned the EagI restriction cleavage site and was countedas part of the cassette D. ^(d)orig/mod: original construct/modifiedcodon-replacement construct. ^(e)Complete capsid region: nt 748 to 3384.^(f)The S2R9 (ABCD) sequence differs from the reference Sabin 2 sequenceat three synonymous third-position sites (see Table 1). ^(g) Does notinclude the 3′-terminal 91 bases of the 5′-UTR at the 5′-end of cassetteA (nt 657 to 747) that were not modified.

Example 3 Growth Properties of Codon-Deoptimized Constructs

This example describes methods used to determine the growth propertiesof the deoptimized Sabin 2 polioviruses generated in Example 2. Similarmethods can be used to determine the replicative fitness of anydeoptimized virus.

Briefly, RNA transcripts of constructs with different combinations ofcodon-replacement cassettes (FIG. 2) were transfected into RD cells asdescribed above. Virus obtained from the primary transfection waspassaged again in RD cells to increase virus titers as described above.The growth properties of the virus constructs in HeLa cells weremeasured by plaque assays (FIGS. 3A-E) and single-step growthexperiments (FIGS. 4A-B).

Plaque assays were performed by a modification of previously describedmethods (Yang et al. J. Virol. 77:8366-77, 2003). Briefly, confluentHeLa cell monolayers in 100 cm² cell culture dishes were washed,inoculated with virus in MEM incomplete, and incubated at roomtemperature for 30 minutes prior to the addition of 0.45% SeaKem LEAgarose (BioWhittaker Molecular, Rockland, Me.) in MEM completecontaining 2% FCS. Plates were incubated for 52-60 hours at 35° C.,fixed with 0.4% formaldehyde and stained with 3% crystal violet. Plaquesize was quantified by scanning plates on a FOTO/Analyst Archiver system(Fotodyne, Hartland, Wis.) and subsequent image analysis using ScionImage for Windows (Scion Corp., Frederick, Md.).

As shown in FIGS. 3A and 3C, an approximately linear inverserelationship was observed between mean plaque area in HeLa cells and thenumber of nucleotide changes in the capsid region. Similar inverselinear relationships were observed when the abscissa was resealed to thenumber of replacement codons (FIG. 3D) or to the number of CGdinucleotides (FIG. 3E). There was no strong polarity to the effects ofcodon replacement within the capsid region, as introduction ofreplacement codons into any combination of the four cassettes reducedplaque areas approximately in proportion to the total number ofreplacement codons. However, replacement of codons into VP1 (cassette D)appeared to have slightly stronger effects than replacement elsewhere.Codon replacement in three or four cassettes generally conferred aminute-plaque phenotype (mean plaque area <25% that of the unmutagenizedABCD prototype), and the mean areas of the observed plaques of the abcdconstruct were ˜9% of the ABCD prototype (FIG. 3C). An exception was theabcD construct, which had a greater mean plaque area (˜38% that of theABCD prototype) than the Abcd, aBcd, and abCd constructs, underscoringthe stronger influence upon plaque size of codon replacement within VP1.

Measurement of plaque areas and total plaque number became difficult asplaque size decreased. The diameters of poliovirus plaques are typicallyheterogeneous, and this heterogeneity was observed with the plaques ofall constructs. Precise measurement was most difficult with the smallestof the minute plaques, as was discriminating very minute plaques fromother small defects in the cell monolayers. Extended incubation ofplaque cultures to 72 hours increased plaque diameters but did notmarkedly increase the plaque counts. Growth properties of all constructswere also determined by plaque assays and limit dilution infectivityassays in HEp-2(C) cells at 35° C. For some of the constructs (abcd,abCD, AbcD, ABcd, and aBCd), the limit dilution infectivity titer was2-10 fold higher than the plaque titers. For the other constructs, limitdilution infectivity and plaque titers were similar. The plaque titersmight have been underestimated for some constructs because of thedifficulty in seeing the tiniest plaques.

A plaque is the result of several cycles of replication, whicheffectively amplifies any difference in replication rate. To determinethe relationship between plaque size, virus growth rates, and virusyield, single-step growth experiments (input MOI: 5 PFU/cell) wereperformed as follows. S3 HeLa suspension cells (1×10⁷) were infected ata multiplicity of infection (MOI) of 5 PFU/cell with stirring for 30minutes at 25° C. After 30 minutes, cells were sedimented by low-speedcentrifugation and resuspended in 2.5 ml warm complete media SMEMcontaining glutamine, 5% FCS, penicillin-streptomycin, and 25 mM HEPES(pH 7.5). Incubation continued at 35° C. in a water bath with orbitalshaking at 300 rpm. Samples were withdrawn at 2-hour intervals from 0 to14 hours postinfection, and titered by plaque assay in Hep-2(C) cells(35° C., 72 hours).

As shown in FIGS. 3B, 4A and 4B, mean virus yields from the single-stepgrowth assays generally decreased as the number of replacement codonsincreased. Virus yields were highest (˜200 PFU/cell) for the ABCDprototype and constructs ABcD and aBCD. Yields were 4- to 8-fold lowerwith constructs ABCd, abCD, and ABcd, 12- to 24-fold lower withconstructs abcD and aBcd, 30- to 45-fold lower with constructs Abcd andabCd, and ˜65-fold lower with construct abcd. Moreover, production ofinfectious virus appeared to be slower in the codon-replacementconstructs than in the unmodified ABCD construct. Although maximumplaque yields were obtained at 10-12 hours for all constructs,proportion of the final yields detected at 4 hours were lower for thecodon-deoptimized constructs (FIGS. 4A and 4B).

In summary, although the Sabin 2 OPV strain has a relatively low codonusage bias, its replicative fitness in cell culture was reduced byreplacement of preferred codons in the capsid region with synonymousunpreferred codons. The reduction in fitness, as measured by plaquearea, was approximately proportional to the length of the intervalcontaining replacement codons. Plaque areas were reduced by ˜90% andvirus burst yields by ˜98% in the abcd construct, in which thereplacement interval spanned nearly the entire capsid region. Thefitness declines in the replacement codon constructs are notattributable to amino acid substitutions because all constructs encodedthe same reference Sabin 2 polyprotein sequence. Virus yields variedover a ˜65-fold range in response to the extent of codon deoptimization.

Multiple synonymous capsid codon replacements increase the ability todetect discernible reductions in poliovirus fitness. For example,replacement of 3 to 14 Arg codons in VP1 (0.3% to 1.6% of capsid codons)with CGG (among the least preferred codons in the poliovirus genome) didnot result in any apparent reduction in plaque areas. The ability todetect small declines in poliovirus fitness might be improved byreplacing the plaque assay, which invariably gives heterogeneousplaques, with a biochemical assay. However, one advantage of the plaqueassay and other virus infectivity assays is their high sensitivities tovery low levels of biological activity.

Example 4 In Vivo Protein Synthesis by Deoptimized Pathogen Sequences

This example describes methods used to determine if there was a changein the amount of protein synthesis due to the presence of deoptimizedcodons. Similar methods can be used to measure protein synthesis by anydeoptimized pathogen sequence.

Monolayer HeLa cells were plated at 8×10⁵ per well in a 6-well dish. Onthe following day, the cells were washed in MEM without serum. Cellswere infected at a multiplicity of infection (moi) of 25 in complete MEMwith 2% serum. Cells were incubated in a CO₂ incubator at 35° C. or 37°C. for 4 hours. Viruses tested were Sabin 2 and MEF1; constructs testedwere S2R9 (Sabin 2 prototype genome; ABCD; SEQ ID NO: 3), S2R19(deoptimized VP3-VP1 genome; ABCd), S2R23 (deoptimized P1/capsid region;abcd; SEQ ID NO: 5), MEF1R2 (MEF1 prototype genome; ABC), MEF1R5(deoptimized VP3-VP1 genome; ABc), and MEF1R9 (deoptimized P1/capsidregion; abc).

Media was removed, and 1.9 ml. of labeling media (200 uCi 35S-met in amixture of 1 volume regular complete MEM containing 2% serum and 7volumes of met-deficient complete MEM containing 2% serum) were added.Cultures were incubated in CO₂ incubator at 35 or 37° C. for 3 hours.Radioactive media was removed, and cells were rinsed twice with PBS.Cells were lysed in 1 ml lysis buffer (10 mM NaCl, 10 mM Tris-Cl pH 7.5,1.5 mM MgCl₂, containing 1% NP-40) at 35° C. for one minute. The lysedcell-media mixture was transferred to a screw-cap Eppendorf tube on ice.0.2 ml. lysis buffer was added to the plate, and this lysate was addedto the original lysate. The lysate was spun at 2000×g 2 minutes 4° C.,and the supernatant was removed to a new tube. SDS was added to the supto make a final concentration of 1% SDS, and samples were frozen.Samples (4 μl) were run on SDS-10% PAGE gels (Laemmli) Gels were fixed,washed, dried on a vacuum gel drier, and exposed to Kodak BioMax filmfor 1-3 days at room temperature.

Although it was thought that replacement of preferred codons withunpreferred codons would lower replicative fitness primarily by reducingthe rate of translation (at the level of polypeptide chain elongation)of viral proteins and potentially disrupting their proteolyticprocessing in infected cells, unexpectedly, it was observed that theelectrophoretic profiles of the labeled virus-specific proteins weresimilar for all S2R viruses, both in the relative intensities of thelabeled viral protein bands and in the total amounts of labeled viralproteins produced in the infected cells (FIG. 5A). The four S2R viruseswere similar in the efficiency of shutoff of host cell protein synthesisand in the synthesis and processing of viral proteins in infected HeLacells. Similar results were obtained with MEF1 viruses (see Example 10,FIG. 5C).

Example 5 In Vitro Translation

This example describes methods used to determine the ability ofdeoptimized poliovirus RNA transcripts to serve as templates for invitro translation in rabbit reticulocyte lysates. Similar methods can beused to measure in vitro protein synthesis by any deoptimized pathogensequence.

For preparation of truncated polio proteins that include the entirecapsid protein and terminate in the 2C noncapsid portion of thepoliovirus genome, plasmid DNAs were digested with SnaBI. Full-lengthand partial viral RNAs were transcribed as described herein. Invitro-transcribed RNAs were subjected to phenol/chloroform extractionand two successive ammonium acetate isopropanol precipitations,including 70% ethanol washes. The RNA pellets were air-dried for 5minutes and then resuspended in a small volume of RNAse-free water. Theresuspended RNA was quantitated by measuring OD260 absorbance in aspectrophotometer.

In vitro translation was performed using a nuclease-treated rabbitreticulocyte lysate (Promega, Madison, Wis.) supplemented with anuninfected HeLa cell extract (Brown and Ehrenfeld Virology 97: 396-405,1979), according to the manufacturer's instructions. The HeLa extracthas been found to improve the fidelity of initiation of translation.Briefly, 35 μl micrococcal nuclease-treated, supplemented rabbitreticulocyte lysate was mixed with 7 μl HeLa cell extract, 1 μl 1 mMamino acid mix (minus methionine), various amounts of RNA (0.2-1 ug), 30μCi³⁵S-met at 15 mCi/ml, and 1 μl RNasin (40 u/ul) in a final volume of50 μl. The reactions were incubated at 30° C. for 3 hours. Samples (4μl) were run on SDS-10% PAGE gels (Laemmli) Gels were fixed, washed,dried on a vacuum gel drier, and exposed to Kodak BioMax film for 1-3days at room temperature.

The efficiency of the poliovirus RNA transcripts to serve as templatesfor in vitro translation in rabbit reticulocytes was similar for all ofthe viruses tested (S2R9, S2R19, S2R23, MEF1R1, MEF1R2, MEF1R5, andMEF1R9). No decline in translational efficiency was observed withincreasing numbers of replacement codons in the in vitro translationsystems tested (FIG. 6). The observation that codon replacement hadlittle detectable effect in vivo upon viral protein synthesis andprocessing was mirrored by the results of in vitro translationexperiments in rabbit reticulocyte lysates. Full-length in vitrotranscripts from cDNA constructs ABCD, ABCd, and abcd (S2R9, S2R19,S2R23), ABC, ABc and abc (MEF1R2, MEF1R5, and MEF1R9) programmed the invitro synthesis and processing of virus-specific proteins with nearlyequal efficiency (FIGS. 5B and 5D). The in vivo and in vitro proteinsynthesis results indicate that the reduced replicative fitness of thecodon-replacement viruses is not primarily attributable to impairment oftranslation and processing of viral proteins.

The protein synthesis results are somewhat surprising, sincetranslational effects have been previously observed when unpreferredcodons were introduced into the coding region of some genes of bacteria(Barak et al., J. Mol. Biol. 256:676-84, 1996), yeast (Hoekema et al.,Mol. Cell Biol. 7:2914-24, 1987), yeast, and one animal virus (Zhou etal., J. Virol. 73:4972-82, 1999). It is possible that translationaleffects were not observed because some of the codons that are rarelyused in poliovirus genomes are used frequently in highly expressedmammalian genes, such that the levels of the tRNAs for these codons maybe high and therefore difficult to deplete. Another possible explanationis that poliovirus RNA is not equivalent to a highly expressed gene, asit is not translated as efficiently as mRNAs of the most highlyexpressed mammalian genes. Polypeptide chain elongation rates are ˜220amino acids per min for poliovirus in HeLa cells at 37° C. (Rekosh, J.Virol. 9:479-87, 1972) compared with ˜600 amino acids per min for theα-chain of hemoglobin in rabbit reticulocytes (Hunt et al., J. Mol.Biol. 43:123-33, 1969). The translation results do not exclude thepossibility that there are local conditions in certain cells in aninfected person or animal that result in decreased translationalefficiency.

Example 6 Specific Infectivities of Virions of Codon-Replacement Viruses

This example describes methods used to measure the infectivity of thedeoptimized Sabin viruses described in Example 2 Similar methods can beused to measure the infectivity of any pathogen with one or moredeoptimized sequences.

Virus was propagated in RD cells, liberated by freeze-thaw, andconcentrated by precipitation with polyethylene glycol 6000 (Nottay etal., Virology 108:405-23, 1981). Virions were purified by pelleting,isopycnic centrifugation in CsCl, and repelleting essentially asdescribed by Nottay et al., (Virology 108:405-23, 1981). The number ofvirus particles in each preparation recovered from the CsCl band with abuoyant density of 1.34 g/ml was calculated from the absorbance at 260nm using the relationship of 9.4×10¹² virions per OD260 unit (Rueckert,R. R. 1976. On the structure and morphogenesis of picornaviruses, p.131-213. In H. Fraenkel-Conrat and R. R. Wagner (ed.), ComprehensiveVirology, vol. 6. Plenum Press, New York.).

The poliovirions produced by HeLa cells infected with viruses ABCD(S2R9), ABCd (S2R19), and abcd (S2R23) were analyzed. Purifiedinfectious virions of all three viruses had similar electrophoreticprofiles and the high VP2/VP0 ratios typical of mature capsids. However,the specific infectivities of the purified virions decreased withincreased numbers of replacement codons. For example, the particle/PFUratios increased from 293 (ABCD) to 1221 (ABCd) to 5392 (abcd). Themagnitude of the decline in specific infectivity was dependent upon theinfectivity assay used, and was steeper with the plaque assay than withthe limit dilution assay. This difference arose because the CCID₅₀/PFUratio in HeLa cells increased with the number of replacement codons,from 1.1 (ABCD) to 5.4 (abcd).

Example 7 Measurement of Viral RNA in Infected Cells

Alterations in the primary sequence of the viral genome could affect thelevels of RNA in infected HeLa cells by modifying the rates of RNAsynthesis or by changing the stabilities of the intracellular viral RNAmolecules. This example describes methods used to measure the amount ofviral RNA produced in cells infected with the deoptimized virusesdescribed in Example 2. However, one skilled in the art will recognizethat similar methods can be used to measure the amount of viral RNAproduced in cells infected with any pathogen with one or moredeoptimized sequences.

Production of viral RNA in infected HeLa cells during the single-stepgrowth assays described above was measured by quantitative RT-PCR usinga Stratagene MX4000 PCR system programmed to incubate at 48° C. for 30min, 95° C. for 10 min, followed by 60 PCR cycles (95° C. for 15 sec,60° C. for 1 min). Sequences within the 3′ half of the 3D^(pol) regionof Sabin 2 were amplified using primers 52/7284A(ATTGGCACACTCCTGATTTTAGC; SEQ ID NO: 59) and S2/7195S(CAAAGGATCCCAGAAACACACA; SEQ ID NO: 60), and the amplicon yield measuredby the fluorescence at 517 nm of the TaqMan probe S2/7246AB(TTCTTCTTCGCCGTTGTGCCAGG; SEQ ID NO: 61) with FAM attached to the 5′ endand BHQ-1 (Biosearch Technologies, Novato, Calif.) attached to the 3′end. Stoichiometric calculations used a value of 2.4×10⁶ for themolecular weight of Sabin 2 RNA (Kitamura, et al., Nature 291:547-53,1981; Toyoda et al., J. Mol. Biol. 174:561-85, 1984).

Total levels of viral RNA present in infected HeLa cells were measuredat 2 h intervals from 0 to 12 hours in the single-step growthexperiments described above and shown in FIGS. 4A and 4B. Viral RNA wasmeasured by quantitative PCR using primers targeting 3D^(pol) sequencesshared among all viruses. After 12 hours, total viral RNA yields werehighest (915 ng/ml; equivalent to ˜57,000 RNA molecules/cell) for ABCD,lower (569 ng/ml; ˜35,000 RNA molecules/cell) for ABCd, and lowest (330ng/ml; ˜20,000 RNA molecules/cell) for abcd (FIG. 6A). Plaque yields, bycontrast, had followed a steeper downward trend, from ˜130 PFU/cell(ABCD), to ˜30 PFU/cell (ABCd), to ˜2 PFU/cell (abcd) (FIGS. 3B and4A-B). Combining these values, the following yields are obtained: ˜440RNA molecules/PFU (ABCD), ˜1200 RNA molecules/PFU (ABCd), and ˜10,000RNA molecules/PFU (abcd). Although the RNA molecules/PFU ratios weresimilar to the particle/PFU ratios determined above for each virus, thenumber of RNA molecules produced in infected cells is typically abouttwice the number of virus particles, because only about 50% of the viralRNA product is encapsidated (Hewlett et al., Biochem. 16:2763-7, 1977).Nonetheless, the two sets of values clearly followed similar trends, asRNA yields and specific infectivities declined with increased number ofreplacement codons.

Because the particle/PFU (or RNA molecule/PFU) ratios were higher forthe codon-replacement viruses than for the unmodified ABCD prototype,substantially more ABCd and abcd virion particles were used to initiatethe single-step growth infections, even though the input MOIs variedover a narrow (˜4-fold) range (FIGS. 4A-B). Consequently, the initialinput RNA levels were high for ABCd and very high for abcd, such thatthe extent of amplification of viral RNA at 12 h was ˜4000-fold forABCD, ˜1000-fold for ABCd, and only ˜20-fold for abcd (FIG. 6).

The observation that the eclipse phases in the single-step growthexperiments were increasingly prolonged as the number of replacementcodons increased indicates that codon-replacement viruses were lessefficient at completing an early step (or steps) of the infectiouscycle. This view is reinforced by the observation that the particle/PFUand RNA molecule/PFU ratios increased sharply with the number ofreplacement codons. It thus appears that a larger number ofcodon-replacement virus particles are needed to initiate a replicativecycle, but once the cycle had started the synthesis and processing ofviral proteins is nearly normal. Although total viral RNA yield wasreduced by only ˜3-fold in the most highly modified abcd virus, itsviral RNA amplification was only ˜20-fold, indicating that impairment ofviral RNA synthesis can also contribute to reduced replicative fitness.

Example 8 RNA Secondary Structures of Codon Deoptimized Sequences

This example describes methods used to predict RNA secondary structuresof the deoptimized Sabin 2 codon genomes generated in Example 2.

Prediction of the secondary structure of the RNA templates of virusconstructs S2R9, S2R19, and S2R23 was performed using the mfold v. 3.1program (Zuker, Science 244: 48-52, 1989; Mathews et al., J. Mol. Biol.288:911-40, 1999; Palmenberg and Sgro, Semin. Virol. 8:231-41, 1997)that implements an energy minimization algorithm that finds a structurelying within a percentage (P) of the calculated minimum energy (MinE).Running parameters were set to default except folding temperature (T),which was set to 35° C. The free energy increment (ΔΔG35° C.), dependenton P, is set to 1 kcal/mol or 12 kcal/mol (SubE₁₂) when the calculatedΔΔG35° C. values lie below or above these values.

The genomic RNAs of polioviruses and other enteroviruses appear to haverelaxed secondary structures outside of the 5′-UTR, the 3′-UTR, and thecre element within the 2C region (Palmenberg and Sgro, Semin. Virol.8:231-41, 1997; Witwer et al., Nucleic Acids Res. 29:5079-89, 2001).Accordingly, under physiological conditions, most bases within the ORFcan pair with more than one partner, and poliovirus genomes can foldinto many different secondary structures having similar thermodynamicstabilities (Palmenberg and Sgro, Semin. Virol. 8:231-41, 1997).However, the incorporation of numerous base substitutions into thecodon-replacement constructs and the concomitant increase in G+C contentmight destabilize folding patterns that had been subject to naturalselection and stabilize other pairings absent from the unmodified Sabin2 genome.

To determine the effects of codon replacement on RNA folding patterns,the secondary structures of the complete genomes of ABCD, ABCd, and abcdwere calculated using the mfold v. 3.1 algorithm. The calculated globalthermodynamic stabilities (expressed as minimum free-energy at 35° C.[ΔG35° C.] or MinE) of the RNA secondary structures increased withincreasing G+C content (ABCD, ΔG35° C.=−2047 kcal/mol; ABCd, ΔG35°C.=−2078 kcal/mol; abcd, ΔG35° C.=−2191 kcal/mol), and the number ofpredicted stem structures increased from 546 (ABCD), to 557 (ABCd), to562 (abcd). The calculated MinE structures for the three viruses alsodiffered (FIG. 7). However, the in vivo pairings are likely to be muchmore flexible and dynamic than indicated by the static structures shownin FIG. 7, as many alternative structures having nearly equivalent (+12kcal/mol) MinE values are predicted (SubE12). A more informative measureof structural rigidity is the p-num value, which gives the number ofalternative pairings for each base. Unaltered in all viruses were thestable (low p-num values, colored red) secondary structures in the5′-UTR, the 3′-UTR, and the cre element, as well as the close appositionof the 5′ and 3′ termini. However, some folding patterns were modifiedin the codon-replacement viruses, and the structural perturbationsextended beyond the boundaries of the modified cassettes. Alterations instable pairings were most extensive with abcd, where the long P1/capsidregion:P3/noncapsid region pairings (nt 1480-1714:nt 5998-5864)predicted for Sabin 2 RNA were destabilized and other pairings formed(FIG. 7).

Example 9 Stability of the Mutant Phenotypes

This example describes methods used to determine the stability of thecodon-deoptimized polioviruses during serial passage in HeLa cells.

Three constructs generated as described in Example 2 were examined: ABCD(unmodified prototype), ABCd (modified VP1 region), and abcd (modifiedP1/capsid region). Poliovirus constructs S2R9 (ABCD), S2R19 (ABCd), andS2R23 (abcd) were serially passaged in HeLa cell monolayers in T75flasks at 35° C. for 36 hours, at an input MOI ranging from 0.1 PFU/cellto 0.4 PFU/cell. Each virus was passaged 25 times (at 35° C. for 36hours), wherein each passage represented at least two rounds ofreplication. At every fifth passage, virus plaque areas, plaque yields,and the genomic sequences of the bulk virus populations were determined,and the MOI was readjusted to ˜0.1 PFU/cell.

All three constructs evolved during serial passage, as measured byincreasing plaque size, increasing virus yield, and changing genomicsequences (Table 3; FIGS. 8A-C). Evolution of the ABCD prototype was theleast complex. Plaque areas increased ˜6-fold from passage 0 to passage15, and this was accompanied by nucleotide substitutions at 6 sites. Bycontrast, virus yields increased 2.5-fold over the 25 passages. Twosubstitutions (U₁₄₃₉→C and C₂₆₀₉→U) were fixed by passage 10, three more(U₃₄₂₄→C, A₃₅₈₆→G, and A₅₅₀₁→G) by passage 15, and all 6 substitutionswere fixed by passage 20. Mixed bases were found at passage 5 (C₁₄₃₉>U,C₂₆₀₉>U, and U₃₄₂₄>C), passage 10 (C₃₄₂₄>U, G₃₅₈₆>>A, and G₅₅₀₁>A) andpassage 15 (A₅₆₃₀>U). No evidence of back mutation or serialsubstitutions at a site was observed.

TABLE 3 Nucleotide substitutions in ABCD, ABCd, and abcd during passage.Amino Nt Nucleotide substitutions −1 Codon +4 acid Location in Virus^(a)Position RD1 HeLa5 HeLa10 HeLa15 HeLa20 HeLa25 nt^(b) change^(c,d,e)nt^(b) subst.^(d) Gene Poly-protein^(f) ABCD 1439 U C > U C C C C CCUU→CCU G L→P VP2 S: NAg-2 2609 C C > U U U U U U GCA→GUA U A→V VP1 I:NC 3424 U U > C C >> U C C C C UAC→CAC A Y→H 2A NC 3586 A A G >> A G G GG AGA→GGA A R→G 2A NC 5501 A A G > A G G G C AAA→AGA G K→R 3C NC 5630 AA A A > U U U U CAG→CUG G Q→L 3C NC ABCd 1456 A A >> G A >> G A > G A =G G > A U AAC→GAC C N→D VP2 S: NAg-2 2776 A A A A > G A > G A > G GAAG→GAG C K→E VP1 S: NAg-1 2780 G G >> A A > G G > A G = A G > A G CG G 

 CAG G R 

 Q VP1 S: NAg-1  3120^(g) G G G G > A A > G >> C A > C >> G U GCG →GCA AA VP1 I: C 3377 C C C C > U C > U C > U A A CG 

 AUG A T 

 M VP1 I: NC 3808 U U U U > C U > C U >> C U UAU→UGU G Y→R 2A NC 3809 AA > G G >> A G = A G > A G >> A 4350 A A > G G > A G = A G > A G = A CUUA 

 UUG U L 2C C abcd 1169 G G G >> A A >> G G > A G > A G CG G 

 CAG A R 

 Q VP2 I: C 1447 A A A A A = G G > A G AAC→GAC G N→D VP2 S: NAg-2 1608 UU U U U = C C > U C GAU→GAC A D VP2 I: C 2622 C C C >> U U >> C C > U CC GU C  

 GU U G V VP1 I: C 2633 C C C U >> C C >> U C U G CG 

 GUG A A 

 V VP1 I: NC 2903 A A A A A = G G > A C AAC→AGC U N→S VP1 S: NAg-1 2915C C C > U C >> U C > U C >> U U G CG 

 GUG A A 

 V VP1 ~S: ~NAg-1 2986 A A A A A = G G > A U AAA→GAA U K→E VP1 I: V 3120^(g) G G > A G = A A >> G A >> G A >> G U GCG →GCA A A VP1 I: NC3121 A A A A >> C A > C A > C G AAA→CAA G K→Q VP1 I: C 3150 G G G A > GG G C ACG →ACA G T VP1 S: NAg-2 3480 U U > G G > U G >> U G G G AGU→AGGG S→R 2A V 4473 G G G A > G A A C AAG→AAA C K 2C C ^(a)Virus constructs:ABCD, S2R9; ABCd, S2R19; abcd, S2R23. ^(b)Nucleotides immediatelypreceding (−1 nt) and immediately following (+4 nt) codon. ^(c)Varyingnucleotide is shown in boldface font. ^(d)Rightward pointing arrowsindicate substitutions that steadily accumulated with increased passage;bidirectional arrows indicate bidirectional fluctuations amongsubstitutions. ^(e)CG dinucleotides, including those across codons, areunderlined. ^(f)Location of amino acid replacements: S, virion surfaceresidue; NAg, neutralizing antigenic site (1, 2); ~NAg, adjacent toneutralizing antigenic site; I, internal capsid residue not exposed tovirion surface; NC, non-consensus amino acid; V, variable amino acid.^(g)Represents direct reversion of engineered codon change.

All substitutions mapped to the coding region, and 2 of 6 (33%) mappedto the capsid region, which represents 35.4% of the genome. In distinctcontrast to the pattern of poliovirus evolution in humans, where thelarge majority of base substitutions generate synonymous codons, all sixof the observed base substitutions (4 at the second codon position and 2at the first codon position) generated amino acid replacements (Table3). None of the substitutions involved loss of a CG dinucleotide.

Evolution of the codon-replacement constructs was more complex anddynamic. In construct ABCd, 4 of the 8 (50%) variable positions mappedto VP1 (12.1% of genome), and 3 of these 4 mapped within thereplacement-codon d interval (9.2% of genome) (Table 3). Substitutionsat half of the positions involved the apparent loss of CG dinucleotides(6.3% of total genome), although in all instances the loss from thevirus population was incomplete. One d interval substitution (G₃₁₂₀→A)eliminating a CG dinucleotide represented a back mutation to theoriginal synonymous codon. A second d interval substitution (G₂₇₈₀→A)reduced the frequency of a CG dinucleotide by HeLa passage 10, but theCG dinucleotide predominated in the population by HeLa passage 25.Another substitution (C₃₃₇₇→U), which resulted in the partial loss of aCG dinucleotide, mapped just downstream from the d interval. Twoadjacent substitutions, mapping to positions 3808 and 3809 in 2A,resulted in a complex pattern of substitution involving first and secondpositions of the same codon. The ABCd construct resembled the ABCDprototype in that substitutions in 6 of the 8 generated amino acidreplacements. By contrast, the ABCd construct differed markedly from theABCD prototype because the dynamics of substitution had apparently notstabilized by passage 25, and mixed bases were found at all 8 positionsof variability (Table 3). The active sequence evolution was accompaniedby progressively increasing plaque areas over a ˜6-fold range, whilevirus yields fluctuated over a narrow (˜2-fold) range (FIGS. 8A-C).

Evolution of the abcd construct was the most dynamic, as determined byexpanding plaque areas, increasing virus yields, and nucleotidesubstitutions. Plaque areas increased ˜15-fold from passage 0 to passage15, and then stabilized (FIGS. 8A-C). Virus yields increased mostsharply (˜4-fold) between passages 5 and 10, but remained ˜4-fold lowerthan those of the ABCD and ABCd constructs at passage 25 (FIG. 8B).Among the 13 sites of nucleotide variability, most (11/13; 84.6%) mappedto the capsid region, all within the codon-replacement interval, 8within VP1, 3 within VP2, and none within VP3 (Table 3). As with theother constructs, most (8/13; 61.5%) of the substitutions encoded aminoacid replacements. Substitutions at six sites involved partial,transient, or complete loss of CG dinucleotides.

As in the ABCd construct, a G₃₁₂₀→A substitution eliminated a CGdinucleotide and restored the original Sabin 2 base. Interestingly, thissame reversion was observed in 8 other independent passages of the abcdconstruct (data not shown). The two variable sites outside of the capsidregion (one in 2A, the other in 2C) stabilized with new substitutions byHeLa passage 20, whereas 8 of the 11 variable sites within the capsidregion still had mixed bases at passage 25. Apart from the back-mutationat position 3120, all other variable sites differed between the ABCD,ABCd, and abcd constructs. No net changes were observed at site A₄₈₁ (inthe 5′-UTR), and U₂₉₀₉ (in the VP1 region), known to be stronglyselected against when Sabin 2 replicates in the human intestine.

In addition to the elimination of several CG dinucleotides, there wasalso a net loss (1 lost, 5 partially lost, 1 gained) of UA dinucleotidesin the high-passage isolates (Table 3). In the codon-replacementconstructs, elimination of UA dinucleotides was incomplete up to passage25. Most (4 of 6) UA losses involved amino acid replacements. Unlikecodons most frequently associated with loss of CG dinucleotides, none ofthe codons associated with loss of UA dinucleotides were replacementcodons. While not as strongly suppressed as CG dinucleotides, UAdinucleotides are underrepresented in poliovirus genomes and humangenes.

Most (8 of 13) of the capsid amino acid replacements mapped within ornear surface determinants forming neutralizing antigenic sites. Forexample, four replacements mapped to NAg-1site and four to NAg-2 site(Table 3). Although surface determinants are generally the mostvariable, amino acid replacements also occurred in naturally variablenon-surface residues in VP1 (Lys→Glu) and 2A^(pro) (Ser→Arg). Most ofthe synonymous mutations mapped to codons for conserved amino acids.However, several of the amino acid replacements, including 5 of the 6 inthe ABCD construct, were substitutions to non-consensus residues (Table3).

Sequence evolution in HeLa cells of the unmodified ABCD virus differedin many respects from the codon-replacement ABCd and abcd viruses.Nucleotide substitutions in the ABCD progeny were dispersed across theORF, dimorphic variants emerged in the early passages, all 6 mutationswere fixed by passage 20, and a single dominant master sequence emerged.By contrast, populations of the ABCd and abcd progeny were complexmixtures of variants at least up to passage 25, and the majority base atthe variable sites typically fluctuated from passage to passage.Apparently the incorporation of unpreferred codons into the ABCd andabcd genomes led to an expansion of the mutant spectrum and to theemergence of complex and unstable quasispecies populations.

To identify potential critical codon replacements, substitutions thataccumulated in the genomes of codon-replacement viruses upon serialpassage in HeLa cells were identified. Only one substitution, G3120→A, adirect back mutation to the original sequence, was shared betweenderivatives of the ABCd and abcd viruses after serial passage. The 19other independent substitutions found among the ABCd and abcdhigh-passage derivatives were associated with 12 different codontriplets. Codon replacement in the VP1 region appeared to haveproportionately greater effects on replicative fitness than replacementsin other capsid intervals, an observation reinforced by the finding that8 of the 13 sites that varied upon serial passage of abcd mapped to theVP1 region. Replacement of VP1 region codons in the genome of theunrelated wild poliovirus type 2 prototype strain, MEF1, also had adisproportionately high impact on growth.

The pattern of reversion among high-passage progeny of thecodon-replacement virus constructs indicates that increased numbers ofCG dinucleotides may contribute to the reductions in fitness. The codonreplacements raised the number of CG dinucleotides in the polioviruscomplete ORFs from 181 (ABCD) to 386 (abcd). Although the biologicalbasis for CG suppression in RNA viruses is poorly understood (Karlin etal., J. Virol. 68:2889-97, 1994), selection against CG dinucleotidesduring serial passage of ABCd and abcd was sufficiently strong at somesites as to drive amino acid substitutions into the normally wellconserved poliovirus capsid proteins. In every instance, the CGsuppression was incomplete, and was frequently reversed upon furtherpassage. The most stable trends toward CG suppression involvednucleotide positions 3120 and 3150 and were not associated with aminoacid changes.

Although fitness of the ABCd and abcd constructs increased during serialpassage in HeLa cells, the virus yields of the ABCd and abcd derivativeswere still below that of the unmodified ABCD construct. In addition, thesubstitutions accumulating in the ABCd and abcd derivatives during cellculture passage were distinct from the Sabin 2 mutations known toaccumulate during propagation in cell culture,

In summary, replicative fitness of both codon-deoptimized and unmodifiedviruses increased with passage in HeLa cells. After 25 serial passages(˜50 replication cycles), most codon modifications were preserved andthe relative fitness of the modified viruses remained below that of theunmodified virus. The increased replicative fitness of high-passagemodified virus was associated with the elimination of several CGdinucleotides.

Codon replacement in VP1 appeared to have greater relative effects onreplicative fitness than replacements in other capsid intervals, anobservation confirmed in similar experiments with the wild poliovirustype 2 prototype strain, MEF1, and reinforced by the finding that 8 ofthe 13 sites that varied upon serial passage of the abcd constructmapped to VP1.

Example 10 Deoptimized Poliovirus MEF1

This example describes methods used to generate a deoptimized MEF1virus, and the effects of deoptimizing the sequence.

Methods used were similar to those for Sabin 2 (see Example 2). FIGS.9A-E show a capsid coding sequence for the poliovirus type 2, strainMEF1 which is deoptimized. The prototype strain is listed on the top(SEQ ID NO: 6), the nucleotide codon change is indicated below that line(SEQ ID NO: 8), and the single-letter amino acid code is included as thethird line (SEQ ID NO: 7).

Replacement codons were introduced into an infectious cDNA clone derivedfrom MEF1 (MEF1R2) within an interval (nt. 748 to 3297) spanning all butthe last 29 codons of the capsid region.

R5 VIRUS Cassette AfeI-XhoI most of VP1 (SEQ ID NO: 54)

R6 VIRUS Cassette EcoRV-AgeI VP4-VP2 (SEQ ID NO: 55)

R7 VIRUS Cassette AgeI-AfeI VP3-partial VP1 (SEQ ID NO: 56)

R8 VIRUS Cassette EcoRV-AfeI VP4-VP2-VP3-partial VP1 (SEQ ID NO: 57)

R9 VIRUS Cassette EcoRV-XhoI Complete capsid (almost) (SEQ ID NO: 58)

Within each cassette, synonymous codons for the nine amino acids werecomprehensively replaced except at 2 positions (replacement at 2 ofthese positions would have generated undesirable restriction sites).Unmodified cassettes were identified by uppercase italic letters; thecorresponding cassettes with modified codons were identified bylowercase italic letters. Thus, the reference MEF1R2 clone wasidentified as ABC (SEQ ID NO: 53), and the fully modified construct(MEF1R9), was identified as abc (SEQ ID NO: 58).

The effect of increasing numbers of replacement codons on growthproperties was similar to that observed for Sabin 2. An approximatelylinear inverse relationship was observed between mean plaque area inHeLa cells and the number of nucleotide changes in the capsid region(FIGS. 9F and 9G). Similar inverse linear relationships were observedwhen the abscissa was resealed to the number of replacement codons or tothe number of CG dinucleotides. There was no strong polarity to theeffects of codon replacement within the capsid region, as introductionof replacement codons into any combination of the three cassettesreduced plaque areas approximately in proportion to the total number ofreplacement codons. However, replacement of codons into VP1 (cassette C)appeared to have slightly stronger effects than replacement elsewhere.Codon replacement across the entire P1/capsid region (construct abc)conferred a minute-plaque phenotype (mean plaque area <25% that of theunmutagenized ABC prototype), and the mean areas of the observed plaquesof the abc construct were ˜6% of the ABC prototype. Replacements in VP3and VP4-VP2 that were ˜86% of the size of the unmutagenized ABCprototype, underscoring the stronger influence upon plaque size of codonreplacement within VP1.

Mean virus yields from the single-step growth assays of MEF1 constructsgenerally decreased as the number of replacement codons increased. Asobserved for the Sabin 2 codon replacement constructs, production ofinfectious virus appeared to be slower in the MEF1 codon-replacementconstructs than in the unmodified ABC construct. Although maximum plaqueyields were obtained at 10-12 hours for all constructs, proportion ofthe final yields detected at 4 hours were lower for thecodon-deoptimized constructs (FIG. 9H). An approximately linear inverserelationship was observed between the log 10 virus yield at 8-12 hourspostinfection in the single-step growth curve in HeLa cells and thenumber of nucleotide changes in the capsid region (FIG. 9I). Plaque sizealso exhibited a linear inverse relationship with the number ofnucleotide changes in the capsid region (FIG. 9J).

The effect on protein translation in vivo and in vitro of thedeoptimized MEF viruses was determined using the methods described inExamples 4 and 5. As was observed for the deoptimized Sabin 2polioviruses, the MEF1 deoptimized viruses had little detectable effectin vivo upon viral protein synthesis and processing (FIG. 5C) or on invitro translation (FIG. 5D).

The effect on RNA yields of the deoptimized MEF viruses was determinedusing the methods described in Example 7, except that the followingprimers were used to RT-PCR the sequence, CTAAAGATCCCAGAAACACTCA andATTGGCACACTTCTAATCTTAGC (SEQ ID NOS: 62 and 63), and amplicon yieldmeasured using CTCTTCCTCGCCATTGTGCCAAG (SEQ ID NO: 64). As was observedfor the deoptimized Sabin 2 polioviruses, RNA yields declined withincreased number of replacement codons. Total viral RNA yields werehighest for ABC, lower for ABc, and lowest for abc (MEF1R9) (FIG. 6B).No increase in viral RNA was observed during the s.s. growth curve forMEF1R9 in HeLa S3 cells.

The MEF1 viruses were purified using the methods described in Example 6.In addition to the virus band at 1.34 g/ml, a large amount of materialwas observed above the virus band. Some of this material was locatedwhere empty capsids might be found in the gradient, but the band wasdiffuse and quite wide. SDS-PAGE analysis of the material revealed VP0,VP1, VP2 and VP3, which is consistent with an immature virus particle.

The ratio of infectivity on RD cells compared to HeLa cells (CCID50)increased as the numbers of nt substitutions increased (Table 4). Theratio for MEF1R2 was 4, whereas the ratio for MEF1R9 was 40. Codondeoptimization had a bigger determinental effect on the virus titermeasured by plaque assay than the virus titer measured by limitingdilution (CCID50) in HeLa cells. For S2R and MEF1R viruses, CCID50titers were higher than PFU titers (Table 4), with S2R23 and MEF1R9having the highest ratios of CCID50/PFU. Codon deoptimization had adramatic effect on the specific infectivity of purified MEF1R viruses,as described for S2R. The particle/HeLa PFU ratios ranged from 182 forMEF1R2 to 18,564 for MEF1R9. The particle/HeLa CCID50s also increasedwith increased numbers of substitutions, but the effect was moremoderate (˜4 fold for MEF1R9).

TABLE 4 Infectivity of native and modified polioviruses RD Virus VirusPurified CCID50/ CCID50/ particles/ particles/ virus HeLa CCID50 PFU(HeLa) HeLa CCID50 HeLa PFU MEF1 1 3 13 63 nonclone MEF1R1 2 5 15 141MEF1R2 4 4 14 182 MEF1R5 6 4 22 368 MEF1R8 4 8 34 692 MEF1R9 40 20 4918564 S2R9 3 6 16 293 S2R19 10 7 25 1221 S2R23 13 16 42 5392

In summary, the replicative fitness of Sabin 2 and MEF1 in cell culturewas reduced by replacement of preferred codons in the capsid region withsynonymous unpreferred codons. The reduction in fitness, as measured byplaque area, was approximately proportional to the length of theinterval containing replacement codons.

Example 11 Additional Deoptimization of Polioviruses

This example describes additional changes that can be made to the Sabin2 poliovirus capsid sequences disclosed in Example 2, or the MEF1poliovirus sequences disclosed in Example 10. Such modified sequencescan be used in an immunogenic composition

In one example, the codon deoptimized Sabin 2 poliovirus capsidsequences disclosed in Example 2 (such as SEQ ID NO: 5), or the codondeoptimized MEF1 poliovirus capsid sequences disclosed in Example 10(such as SEQ ID NO: 58) can be further deoptimized. For example,additional codon substitutions (for example AUA (Ile), AAA (Lys), andCAU (His)), as well as and redesigned codon substitutions (for exampleUCG (Ser)) codon substitutions, which are better matched to the leastabundant tRNA genes in the human genome (International Human GenomeSequencing Consortium. Nature 409:860-921, 2001), can be used to furtherimpair translational efficiency and reduce replicative fitness. Suchsubstitutions can be made using routine molecular biology methods.

Example 12 Additional Methods to Decrease Replicative Fitness

This example describes additional or alternative substitutions that canbe made to a pathogen sequence to increase the replicative fitness of apathogen. In addition to changing codon usage, alterations in G+Ccontent and the frequency of CG or TA dinucleotide pairs can be used todecrease the replicative fitness of a pathogen. For example, a pathogensequence that includes one or more deoptimized codons can furtherinclude an alteration in the overall G+C content of the sequence, suchas an increase or decrease of at least 10% in the G+C content in thecoding sequence (for example without altering the amino acid sequence ofthe encoded protein). In another or additional example, a pathogensequence that includes one or more deoptimized codons can furtherinclude an alteration in the number of CG or TA dinucleotides in thesequence, such as an increase or decrease of at least 20% in the numberof CG or TA dinucleotides in the coding sequence.

Altering G+C Content

The replicative fitness of a pathogen can be altered by changing the G+Ccontent of a pathogen coding sequence. For example, to increase the G+Ccontent, codons used less frequently by the pathogen that include a “G”or “C” in the third position instead of an “A” or “T” can beincorporated into the deoptimized sequence. Such methods can be used incombination with the other methods disclosed herein for decreasingreplicative fitness of a pathogen, for example in combination withdeoptimizing codon sequences or altering the frequency of CG or TAdinucleotides.

In one example, the G+C content of a pathogen coding sequence is reducedto decrease replicative fitness. For example, the G+C content of arubella virus coding sequence can be reduced to decrease replicativefitness of this virus. In one example, the G+C content of a rubellasequence is decreased by at least 10%, at least 20%, or at least 50%,thereby decreasing replicative fitness of the virus. Methods ofreplacing C and G nucleotides as well as measuring the replicativefitness of the virus are known in the art, and particular examples areprovided herein.

In another example, the G+C content of a pathogen coding sequence isincreased to decrease replicative fitness. For example, the G+C contentof a poliovirus coding sequence can be reduced to decrease replicativefitness of this virus. In one example, the G+C content of a poliovirussequence is increased by at least 10%, at least 20%, or at least 50%,thereby decreasing replicative fitness of the virus. Methods ofreplacing A and T nucleotides with C and G nucleotides are known in theart, and particular examples are provided herein.

Altering Frequency of CG or TA Dinucleotides to Decrease ReplicativeFitness

The replicative fitness of a pathogen can be altered by changing thenumber of CG dinucleotides, the TA dinucleotides, or both, in a pathogencoding sequence. For example, to increase the number of CG dinucleotidesin a deoptimized sequence, codons used less frequently by the pathogenthat include a CG in the second and third position instead of anotherdinucleotide can be incorporated into the deoptimized sequence. Suchmethods can be used in combination with the other methods disclosedherein for decreasing replicative fitness of a pathogen, for example incombination with deoptimizing codon sequences.

The dinucleotides CG and TA (UA) are known to be suppressed inpoliovirus genomes (Karlin et al., J. Virol. 68:2889-97; Kanaya et al.,J. Mol. Evol. 53, 290-8; Toyoda et al. J. Mol. Biol. 174:561-85). Theresults described herein with the Sabin 2 constructs indicate thatincreased numbers of CG and TA dinucleotides are associated withreductions in replicative fitness. Therefore, the number of CG or TAdinucleotides can be increased in polio and other eukaryotic viruses(such as those in which CG is strongly suppressed in the genome) todecrease their replicative fitness. In one example, the number of CG orTA dinucleotides in a virus sequence is increased by at least 10%, atleast 30%, at least 100%, or at least 300%, thereby decreasingreplicative fitness of the virus. The number of CG dinucleotides, TAdinucleotides, or both can be increased in a viral sequence usingroutine molecular biology methods, and using the methods disclosedherein. For example, additional CG dinucleotides can be incorporatedinto the ORF by uniform replacement of degenerate third-position baseswith C when the first base of the next codon is G. Replacement of codonsspecifying conserved amino acids can be used to further stabilize thereduced fitness phenotype, as restoration of fitness may strictlyrequire synonymous mutations.

Exemplary Sequences

Provided herein are exemplary modified Sabin 2 sequences that havesilent (synonymous) nucleotide substitutions in the cassette d (VP1region). Such modified sequences can be used in an immunogeniccomposition

SEQ ID NO: 65 (and FIG. 25) show a Sabin 2 sequence with a reducednumber of CG dinucleotides (number of CG dinucleotides reduced by 94%).SEQ ID NO: 66 (and FIG. 26) show a Sabin 2 sequence with a reducednumber of both CG dinucleotides and UA dinucleotides (number of CGdinucleotides reduced by 94% and number of TA dinucleotides reduced by57%). These sequences will likely have similar replicative fitness as anative poliovirus, and therefore can be used as a control.

SEQ ID NO: 67 (and FIG. 27) show a Sabin 2 sequence with an increasednumber of CG dinucleotides (number of CG dinucleotides increased by389%). SEQ ID NO: 68 (and FIG. 28) show a Sabin 2 sequence with anincreased number of both CG dinucleotides and UA dinucleotides, with apriority placed on increasing CG dinucleotides (number of CGdinucleotides increased by 389% and number of TA dinucleotides increasedby 203%). These sequences will likely have reduced replicative fitnesscompared to a native poliovirus, and therefore can be used inimmunogenic compositions.

SEQ ID NO: 69 (and FIG. 29) show a Sabin 2 sequence having maximum codondeoptimization. In this sequence, the least favored codons were selectedwithout reference to CG or TA dinucleotides. This sequences will likelyhave reduced replicative fitness compared to a native poliovirus, andtherefore can be used in an immunogenic composition.

SEQ ID NO: 70 (and FIG. 30) show a Sabin 2 sequence using MEF1 codonsfor Sabin 2 amino acids. This provides a means of using different,naturally occurring codons. This sequences will likely have similarreplicative fitness as a native poliovirus, and therefore can be used asa control.

Example 13 Determination of the Replication Steps Altered in HighlyModified Viruses

This example describes methods that can be used to identify thedefective replication step in a virus whose coding sequence has beenaltered to reduce replicative fitness of the virus.

A modified virus, such as a highly modified viruses (for example S2R23(SEQ ID NO: 5) and MEF1R9 (SEQ ID NO: 58)) can be screened using routinemethods in the art. For example, the effects of deoptimizing codons onvirus binding, eclipse, uncoating, and particle elution steps can bedetermined using known methods (Kirkegaard, J. Virol. 64:195-206 andLabadie et al. Virology 318:66-78, 2004, both herein incorporated byreference as to the methods). Briefly, binding assays (Kirkegaard, J.Virol. 64:195-206) could involve determining the percentage of³H-labeled virions onto HeLa or other cells. After incubation with³H-labeled purified poliovirus (such as those shown in SEQ ID NOS: 5 and58), cells are washed extensively with PBS and the initial and remainingradioactivity counts determined by tricholoroacetic acid precipitationand filtering of the labeled particles.

For conformational alteration assays (Kirkegaard, J. Virol. 64:195-206),polioviruses (such as those shown in SEQ ID NOS: 5 and 58) are preboundto a HeLa monolayer at 4° C. for 60 minutes at MOIs of 0.1 PFU/cell. Themonolayers are washed three times with PBS and incubated for varioustime periods at 35° C. Cells are harvested by scraping, and cytoplasmicextracts are titered by plaque assay on HeLa cells. An alternate method(Pelletier et al., Virol. 305:55-65) is to use [³⁵S]-methionine-labeledpurified virus particles. Infections are synchronized by a 2.5-hourperiod of adsorption at 0° C., and then conformational transitionsinitiated by incubation at 37° C. for 3 or 10 minutes. Cell-associatedvirus particles are separated by centrifugation in sucrose gradients(15-30% w/v) (Pelletier et al., Cell. Mol. Life Sci. 54:1385-402, 1998).

For RNA release assays (Kirkegaard, J. Virol. 64:195-206), neutralred-containing virus is prepared by harvesting virus (such as thoseshown in SEQ ID NOS: 5 and 58) from HeLa monolayer grown in the presenceof 10 μg of neutral red per ml. Time courses of RNA release aredetermined by pre-binding approximately 200 PFU of each virus to HeLamonolayers at 4° C. for 60 minutes, followed by washing twice with PBS,and agar overlay. Duplicate plates are irradiated for 8 minutes aftervarious times of incubation at 35° C. The numbers of plaques on theirradiated plates are expressed as a percentage of the number of plaqueson the unirradiated control.

Protein synthesis and the kinetics of host cell shutoff of proteinsynthesis can be determined by using pulse-chase experiments in infectedcells and other standard methods. Pactamycin will be used to studytranslational elongation rates (Rekosh, J. Virol. 9:479-487). Thespectrum of virus particles produced by highly modified viruses can becharacterized using fractions from a CsCl density gradient.

Infectivities in different cell types, such as Vero (African greenmonkey cell line) and human (and possibly murine) neuroblastoma celllines, can also be determined using routine methods, such as thosedisclosed herein.

Example 14 Deoptimized Picornaviruses

Examples 14-17 describe methods that can be used to generate adeoptimized positive-strand RNA virus. This example describes methodsthat can be used to generate a deoptimized Picornavirus sequence, whichcan be used in an immunogenic composition. Particular examples offoot-and-mouth disease virus (FMDV) and polioviruses are described.However, one skilled in the art will appreciate that similar (and insome examples the same) substitutions can be made to any Picornavirus.

Sequences for FMDV are publicly available (for example see GenBankAccession Nos: AJ539141; AY333431; NC_003992; NC_011452; NC_004915;NC_004004; NC_002554; AY593852; AY593851; AY593850; and AY593849). Usingpublicly available FMDV sequences, along with publicly available codonusage tables from FMDV (for example see Sanchez et al., J. Virol.77:452-9, 2003; and Boothroyd et al., Gene 17:153-61, 1982, hereinincorporated by reference and FIG. 24A), one can generate deoptimizedFMDV sequences.

Using the methods described above in Examples 1 and 2, the capsid ofFMDV can be deoptimized. FIGS. 10A-B (and SEQ ID NO: 11) show anexemplary FMDV, serotype O strain UKG/35/2001 capsid sequence havingcodons deoptimized for 9 amino acids (see Table 5). FMDV containingthese substitutions can be generated using standard molecular biologymethods. In addition, based on the deoptimized codons provided in Table5, one or more other FMDV coding sequences can be deoptimized. Inaddition, the methods described in Example 12 can be used to alter theG+C content or the number of CG or TA dinucleotides in an FMDV codingsequence, for example to further decrease the replicative fitness ofFMDV.

TABLE 5 Deoptimized FMDV codons Amino acid Deoptimized codon Pro CCG ValGTA Gly GGG Ala GCG Ile ATA Thr ACG Leu CTA Ser TCG Arg CGA

Sequences for poliovirus are publicly available (for example see GenBankAccession Nos: AF111984; NC_002058; AY560657; AY278553; AY278552;AY278551; AY278550; AY27849; AF538843; AF538842; AF538840; AY177685;AY184221; AY184220; AY184219; and AY238473). Using publicly availablehuman poliovirus sequences, along with publicly available codon usagetables for poliovirus (Rothberg and Wimmer, Nucleic Acids Res. 9:6221-9,1981, as well as the tables disclosed herein), one can generatedeoptimized poliovirus sequences.

Using the methods described above (for example see Examples 1 and 2),the capsid of poliovirus can be deoptimized FIGS. 9A-E (SEQ ID NO: 8)shows an exemplary poliovirus type 2, strain MEF1 capsid sequence havingall Arg codons deoptimized to CGG. Poliovirus containing thesesubstitutions can be generated using standard molecular biology methods.

Similarly, using the methods described above (for example, see Examples1 and 2), poliovirus types 1 and 3 can be deoptimized (for example bydeoptimization of the capsid sequence). For example, the neurovirulentwild strains type 1 Mahoney/USA41 (POLIO1B; GenBank Accession No:V01149) and type 3 Leon/USA37 (POL3L37; GenBank Accession No: K01392),and their Sabin strain derivatives LSc tab (Sabin type 1) (GenBankAccession No: V01150), and Leon 12 a₁b (Sabin type 3) (GenBank AccessionNo: X00596) can be deoptimized.

Example 15 Deoptimized Coronaviruses

This example describes methods that can be used to generate adeoptimized Coronavirus sequence, which can be used in an immunogeniccomposition. A particular example of a SARS virus is described. However,one skilled in the art will appreciate that similar (and in someexamples the same) substitutions can be made to any Coronavirus.

Sequences for SARS are publicly available (for example, see GenBankAccession Nos: NC_004718; AY654624; AY595412; AY394850; AY559097;AY559096; AY559095; AY559094; AY559093; AY559092; AY559091; AY559090;AY559089; AY559088; AY274119; and AY278741). Using publicly availableSARS sequences, along with publicly available codon usage tables fromSARS (for example, see Rota et al., Science 300:1394-1399, 2003, hereinincorporated by reference, and FIG. 24B), one can generate deoptimizedSARS sequences.

Using the methods described above in Examples 1 and 2, the spikeglycoprotein of SARS can be deoptimized FIGS. 11A-C (and SEQ ID NO: 14)shows an exemplary SARS, strain Urbani spike glycoprotein sequencehaving codons deoptimized for 9 amino acids (see Table 6). SARScontaining these substitutions can be generated using standard molecularbiology methods. In addition, based on the deoptimized codons providedin Table 6, one or more SARS coding sequences can be deoptimized.Furthermore, the methods described in Example 12 can be used to alterthe G+C content or the number of CG or TA dinucleotides in an SARScoding sequence, for example to further decrease the replicative fitnessof SARS.

TABLE 6 Deoptimized SARS codons Amino acid Deoptimized codon Pro CCG ValGTC Gly GGG Ala GCG Ile ATC Thr ACG Leu CTG Ser TCG Arg CGG

Example 16 Deoptimized Togaviruses

This example describes methods that can be used to generate adeoptimized togavirus sequence, which can be used in an immunogeniccomposition. A particular example of a rubella virus is described.However, one skilled in the art will appreciate that similar (and insome examples the same) substitutions can be made to any togavirus.

Sequences for rubella virus are publicly available (for example seeGenBank Accession Nos: L78917; NC_001545; AF435866; AF188704 andAB047329). Using publicly available rubella sequences, along withpublicly available codon usage tables from rubella virus (for examplesee Nakamura et al., Nucleic Acids Res. 28:292, 2000 and FIG. 24C), onecan generate deoptimized rubella virus sequences. Similar methods can beused to generate a deoptimized sequence for any togavirus.

Using the methods described above in Examples 1 and 2, the codingsequence of a togavirus can be deoptimized. FIGS. 12A-G (and SEQ ID NO:18) shows an exemplary rubella virus sequence having codons deoptimizedfor 10 amino acids (see Table 7). Rubella viruses containing thesubstitutions shown in FIG. 11 can be generated using standard molecularbiology methods. In addition, based on the deoptimized codons providedin Table 7, one or more other rubella coding sequences can bedeoptimized. Furthermore, the methods described in Example 12 can beused to alter the G+C content or the number of CG or TA dinucleotides ina rubella coding sequence, for example to further decrease thereplicative fitness of rubella.

TABLE 7 Deoptimized rubella codons Amino acid Deoptimized codon Gly GGAAla GCA Val GTA Thr ACA Cys TGT Tyr TAT Leu TTA Ser TCA Arg AGA Pro CCA

Example 17 Deoptimized Flaviviruses

This example describes methods that can be used to generate adeoptimized flavivirus sequence, which can be used in an immunogeniccomposition. Particular examples of a Dengue I and Dengue II viruses aredescribed. However, one skilled in the art will appreciate that similar(and in some examples the same) substitutions can be made to anyflavivirus.

Sequences for Dengue type 1 and Dengue type 2 virus are publiclyavailable (for example see GenBank Accession Nos: M87512; U88535 andU88536 for type 1 and M19197; M29095 and AF022434 for type 2). Usingpublicly available Dengue 1 and Dengue 2 sequences, along with publiclyavailable codon usage tables from Dengue type 1 and Dengue type 2 virus(for example see Nakamura et al., Nucleic Acids Res. 28:292, 2000 andFIGS. 22 D and E, respectively), one can generate deoptimized Denguetype I and Dengue type II virus sequences. Similar methods can be usedto generate a deoptimized sequence for any flavivirus.

Using the methods described above in Examples 1 and 2, the codingsequence of a flavivirus can be deoptimized. Flaviviruses, such asDengue type 1 and 2 viruses, containing these substitutions can begenerated using standard molecular biology methods, based on thedeoptimized codons provided in Tables 8 and 9. Furthermore, the methodsdescribed in Example 12 can be used to alter the G+C content or thenumber of CG or TA dinucleotides in a Flavivirus coding sequence, forexample to further decrease the replicative fitness of the Flavivirus.

TABLE 8 Deoptimized dengue type 1 codons Amino acid Deoptimized codonGly GGC Ala GCG Val GTA Thr ACG Leu CTC Ser TCG Arg CGG Pro CCG

TABLE 9 Deoptimized dengue type 2 codons Amino acid Deoptimized codonGly GGT Ala GCG Val GTA Thr ACG Leu CTT Ser TCG Arg CGG Pro CCG

Example 18 Deoptimized Herpesviruses

This example describes methods that can be used to generate adeoptimized herpesvirus sequence, which can be used in an immunogeniccomposition. A particular example of a varicella-zoster virus (humanherpesvirus 3) is described. In addition, provided is a list ofdeoptimized codon sequences that can be used for HSV-1 or HSV-2, as wellas human cytomegalovirus (CMV; human herpesvirus 5). However, oneskilled in the art will appreciate that similar (and in some examplesthe same) substitutions can be made to any herpesvirus.

Sequences for varicella-zoster virus are publicly available (for examplesee GenBank Accession Nos: NC_001348; AY548170; AY548171; AB097932 andAB097933). Using publicly available varicella-zoster virus sequences,along with publicly available codon usage tables from varicella-zostervirus (for example see Nakamura et al., Nucleic Acids Res. 28:292, 2000and FIG. 24F), one can generate deoptimized varicella-zoster virussequences.

Using the methods described above in Examples 1 and 2, the gH and gEcoding sequence of a herpesvirus can be deoptimized. FIGS. 13A-B and14A-B (and SEQ ID NOS: 21 and 24) show exemplary varicella-zoster virusgH and gE sequences having codons deoptimized for 9 amino acids (seeTable 10). Varicella-zoster virus containing these substitutions can begenerated using standard molecular biology methods. Using the methodsdescribed above in Examples 1 and 2, and standard molecular biologymethods, the coding sequence of one or more VZV genes can bedeoptimized. In addition, based on the deoptimized codons provided inTable 10, one or more other VZV coding sequences can be deoptimized.Furthermore, the methods described in Example 12 can be used to alterthe G+C content or the number of CG or TA dinucleotides in a VZV codingsequence, for example to further decrease the replicative fitness of theVZV.

TABLE 10 Deoptimized varicella-zoster codons Amino acid Deoptimizedcodon Pro CCT Val GTC Gly GGC Ala GCT Ile ATC Thr ACT Leu CTA Ser AGTArg AGG

Sequences for human cytomegalovirus (CMV; human herpesvirus 5) arepublicly available (for example see GenBank Accession Nos: AY446894;BK000394; AC146999; NC_001347; and AY315197). Using publicly availableCMV sequences, along with publicly available codon usage tables from CMV(for example see Nakamura et al., Nucleic Acids Res. 28:292, 2000 andFIG. 24G), one can generate deoptimized CMV sequences.

Table 11 shows CMV deoptimized codon sequences for 9 amino acids. Thecomplete genome of CMV is about 233-236 kb. Using the methods describedabove in Examples 1 and 2, and standard molecular biology methods,glycoprotein B (UL55), glycoprotein H (UL75), and glycoprotein N (UL73)coding sequences of a CMV can be deoptimized. In addition, based on thedeoptimized codons provided in Table 11, one or more other CMV codingsequences can be deoptimized. Furthermore, the methods described inExample 12 can be used to alter the G+C content or the number of CG orTA dinucleotides in a CMV coding sequence, for example to furtherdecrease the replicative fitness of CMV.

TABLE 11 Deoptimized CMV codons Amino acid Deoptimized codon Pro CCA ValGTT Gly GGG Ala GCA Ile ATA Thr ACA Leu TTA Ser TCA Arg AGG

Sequences for herpes simplex virus 1 and 2 (HSV1 and HSV2) are publiclyavailable (for example see GenBank Accession Nos: X14112 and NC_001806for HSV1 and NC_001798 for HSV2). Using publicly available HSV1 and HSV2sequences, along with publicly available codon usage tables from HSV1and HSV2 (for example see Nakamura et al., Nucleic Acids Res. 28:292,2000 and FIG. 24H), one can generate deoptimized HSV1 and HSV2sequences.

Table 12 shows HSV1 and HSV2 deoptimized codon sequences for 11 aminoacids. The codon choices for HSV1 and 2 are very similar and where thereare differences they are small. Therefore, the same codon choices can beused for both HSV1 and HSV2. The complete genome of HSV1 and HSV2 isabout 152 kb and 155 kb, respectively. Using the methods described abovein Examples 1 and 2, and standard molecular biology methods,glycoprotein B (UL27), glycoprotein D (US6), tegument protein hostshut-off factor (UL41; see Geiss, J. Virol. 74:11137, 2000), andribonucleotide reductase large subunit (UL39; see Aurelian, Clin. Diag.Lab. Immunol. 11:437-445, 2004) coding sequences of HSV1 or HSV2 can bedeoptimized. In addition, based on the deoptimized codons provided inTable 12, one or more other HSV1 or HSV2 coding sequences can bedeoptimized. Furthermore, the methods described in Example 12 can beused to alter the G+C content or the number of CG or TA dinucleotides ina HSV1 or HSV2 coding sequence, for example to further decrease thereplicative fitness of HSV1 or HSV2.

TABLE 12 Deoptimized HSV1 and HSV2 codons Codon HSV1 HSV2 Pro CCT CCAVal GTA GTA Gly GGA GGT Ala GCT GCA Ile ATA ATA Thr ACT ACT Leu TTA TTASer TCA TCA Arg AGA AGA Asn AAT AAT Asp GAT GAT

Example 19 Deoptimized Paramyxoviruses

Examples 19 and 20 describe methods that can be used to generate adeoptimized negative-strand RNA virus. This example describes methodsthat can be used to generate a deoptimized paramyxovirus sequence, whichcan be used in an immunogenic composition. Particular examples ofmeasles and respiratory syncytial viruses (RSV) are described. However,one skilled in the art will appreciate that similar (and in someexamples the same) substitutions can be made to any paramyxovirus.

Sequences for measles and RSV are publicly available (for example seeGenBank Accession Nos: NC_001498; AF266287; AY486084; AF266291; andAF266286 for measles; and NC_001781; U63644; AY353550; NC_001803;AF013254 and U39661 for RSV). Using publicly available measles and RSVsequences, along with publicly available codon usage tables from measlesand RSV (for example see Nakamura et al., Nucleic Acids Res. 28:292,2000 and FIG. 24I), one can generate deoptimized measles and RSVsequences. Similar methods can be used to generate a deoptimizedsequence for any paramyxovirus.

Using the methods described above in Examples 1 and 2, the fusion (F) orhemagglutinin (H) coding sequence of a paramyxovirus can be deoptimized.FIGS. 15A-B and 16A-B show exemplary measles F and G sequences havingcodons deoptimized for 8 amino acids (SEQ ID NOS: 27 and 30,respectively). FIGS. 17A-B and 18 (and SEQ ID NOS: 33 and 36) showexemplary RSV F and glycoprotein (G) sequences having codons deoptimizedfor 8 amino acids (see Tables 13 and 14). Measles and RSV virusescontaining these substitutions can be generated using standard molecularbiology methods. In addition, based on the deoptimized codons providedin Tables 13 and 14, one or more other measles or RSV coding sequencescan be deoptimized. Furthermore, the methods described in Example 12 canbe used to alter the G+C content or the number of CG or TA dinucleotidesin a RSV coding sequence, for example to further decrease thereplicative fitness of RSV.

TABLE 13 Deoptimized measles codons Amino acid Deoptimized codon Gly GGCAla GCG Val GTA Thr ACG Leu CTT Ser TCG Arg CGC Pro CCG

TABLE 14 Deoptimized RSV codons Amino acid Deoptimized codon Gly GGG GluGAG Ala GCG Thr ACG Leu CTG Ser TCG Arg CGG Pro CCG

Example 20

Deoptimized Orthomyxyoviruses

This example describes methods that can be used to generate adeoptimized orthomyxyovirus sequence, which can be used in animmunogenic composition. A particular example of an influenza virus isdescribed. However, one skilled in the art will appreciate that similar(and in some examples the same) substitutions can be made to anyorthomyxyovirus.

Sequences for influenza virus are publicly available (for example seeNC_002204 and AY253754). Using publicly available influenza sequences,along with publicly available codon usage tables from influenza (forexample see Nakamura et al., Nucleic Acids Res. 28:292, 2000 and FIG.24J), one can generate deoptimized influenza sequences. Similar methodscan be used to generate a deoptimized sequence for any orthomyxyovirus.

Using the methods described above in Examples 1 and 2, the hemagglutinin(HA) or neuraminidase (NA) coding sequences of an orthomyxyovirus can bedeoptimized. FIGS. 17 and 18 show an exemplary influenza virus HA (FIG.19 and SEQ ID NO: 39) and a NA gene (FIG. 20 and SEQ ID NO: 42) sequencehaving codons deoptimized for 8 amino acids (see Table 15). Influenzaviruses containing these substitutions can be generated using standardmolecular biology methods. In addition, based on the deoptimized codonsprovided in Table 15, one or more other influenza coding sequences canbe deoptimized. Furthermore, the methods described in Example 12 can beused to alter the G+C content or the number of CG or TA dinucleotides inan influenza coding sequence, for example to further decrease thereplicative fitness of influenza.

TABLE 15 Deoptimized influenza codons Amino acid Deoptimized codon GlyGGC Ala GCG Ile ATC Thr ACG Leu TTA Ser TCG Arg CGC Pro CCG

Example 21 Deoptimized Retroviral Codons

This example describes methods that can be used to generate adeoptimized retrovirus sequence, which can be used in an immunogeniccomposition. Particular examples of an HIV type 1 (HIV-1), subtype C,retrovirus, and a lentivirus, are described. However, one skilled in theart will appreciate that similar (and in some examples the same)substitutions can be made to any retrovirus.

Sequences for HIV-1 are publicly available (for example see GenBankAccession Nos: AF110967; AY322191; AY682547; AY536234; AY536238;AY332236; AY331296 and AY331288). Using publicly available HIV-1sequences, along with publicly available codon usage tables from HIV-1(for example see Nakamura et al., Nucleic Acids Res. 28:292, 2000; Chouand Zhang, AIDS Res. Hum. Retroviruses. 8:1967-76, 1992; Kyprand Mrazek,Nature. 327(6117):20, 1987, all herein incorporated by reference, andFIG. 24K), one can generate deoptimized HIV-1 sequences. Similar methodscan be used to generate a deoptimized sequence for any retrovirus.

Using the methods described above in Examples 1 and 2, the env codingsequence of HIV-1 can be deoptimized. FIGS. 21A-B (and SEQ ID NO: 45)shows an exemplary HIV-1 env sequence having codons deoptimized for 8amino acids (see Table 16). HIV-1 containing these substitutions can begenerated using standard molecular biology methods. In addition, basedon the deoptimized codons provided in Table 16, one or more other HIV-1coding sequences can be deoptimized. Furthermore, the methods describedin Example 12 can be used to alter the G+C content or the number of CGor TA dinucleotides in an HIV-1 coding sequence, for example to furtherdecrease the replicative fitness of HIV-1.

TABLE 16 Deoptimized HIV-1 codons Amino acid Deoptimized codon Gly GGTAla GCG Val GTC Thr ACG Leu CTC Ser TCG Arg CGT Pro CCG

The equine infectious anemia virus (EIAV) is a lentivirus. Sequences forEIAV are publicly available (for example see GenBank Accession Nos:M87581; X16988; NC_001450 and AF327878). Using publicly available EIAVsequences, along with publicly available codon usage tables from EIAV(for example see Nakamura et al., Nucleic Acids Res. 28:292, 2000,herein incorporated by reference, and FIG. 24L), one can generatedeoptimized EIAV sequences. Similar methods can be used to generate adeoptimized sequence for any lentivirus.

Using the methods described above in Examples 1 and 2, the env codingsequence of EIAV can be deoptimized, for example using the deoptimizedcodons provided in Table 17. Furthermore, the methods described inExample 12 can be used to alter the G+C content or the number of CG orTA dinucleotides in an EIAV coding sequence, for example to furtherdecrease the replicative fitness of EIAV.

TABLE 17 Deoptimized equine infectious anaemia virus (EIAV) codons Aminoacid Deoptimized codon Gly GGC Ala GCG Val GTC Thr ACG Leu CTC Ser TCGArg CGC Pro CCG

Example 22 Deoptimized Bacterial Codons

This example describes methods that can be used to generate adeoptimized bacterial sequence, which can be used in an immunogeniccomposition. Particular optimized E. coli sequences are described.However, one skilled in the art will appreciate that similar (and insome examples the same) substitutions can be made to any bacterialcoding sequence.

Sequences for E. coli are publicly available (for example see GenBankAccession Nos: NC_002695; NC_000913; BA000007; NC_004431; and AE014075).Using publicly available E. coli sequences, along with publiclyavailable codon usage tables from E. coli (for example see Nakamura etal., Nucleic Acids Res. 28:292, 2000 and Sharp et al., Nucleic AcidsRes. 16:8207-11, 1988, all herein incorporated by reference, and FIG.24M), one can generate deoptimized E. coli sequences Similar methods canbe used to generate a deoptimized sequence for any bacterium.

Using the methods described above in Examples 1 and 2, the ArgS or TufAcoding sequences of E. coli can be deoptimized. FIGS. 22A-B and 23 showsexemplary E. coli ArgS and TufA sequences (and SEQ ID NOS: 48 and 51),respectively, having codons deoptimized for 1 amino acid. E. colicontaining these substitutions can be generated using standard molecularbiology methods. In addition, based on the deoptimized codon provided inTable 18, one or more other E. coli coding sequences can be deoptimized.Furthermore, the methods described in Example 12 can be used to alterthe G+C content or the number of CG or TA dinucleotides in an E. colicoding sequence, for example to further decrease the replicative fitnessof E. coli.

TABLE 18 Deoptimized E. coli K12 codon Amino acid Deoptimized codon ArgAGG

Example 23 Pharmaceutical Compositions

The disclosed immunogenic deoptimized pathogenic sequences can beincorporated into pharmaceutical compositions (such as immunogeniccompositions or vaccines). Pharmaceutical compositions can include oneor more deoptimized pathogenic sequences and a physiologicallyacceptable carrier. Pharmaceutical compositions also can include animmunostimulant. An immunostimulant is any substance that enhances orpotentiates an immune response to an exogenous antigen. Examples ofimmunostimulants include adjuvants, biodegradable microspheres (such aspolylactic galactide microspheres) and liposomes (see, for example, U.S.Pat. No. 4,235,877). Vaccine preparation is generally described, forexample, in M. F. Powell and M. J. Newman, eds., Vaccine Design: thesubunit and adjuvant approach, Plenum Press, N Y, 1995. Pharmaceuticalcompositions within the scope of the disclosure can include othercompounds, which may be either biologically active or inactive.

A pharmaceutical composition can include DNA having a deoptimized codingsequence. The DNA can be present within any of a variety of deliverysystems known to those of ordinary skill in the art, including nucleicacid expression systems, bacteria and viral expression systems. Numerousgene delivery techniques are well known in the art, including thosedescribed by Rolland, Crit. Rev. Therap. Drug Carrier Systems 15:143-198, 1998, and references cited therein. Appropriate nucleic acidexpression systems contain DNA sequences for expression in the subject(such as a suitable promoter and terminating signal). Bacterial deliverysystems involve the administration of a bacterium (such asBacillus-Calmette-Guerrin) that expresses the polypeptide on its cellsurface or secretes it. In one example, the DNA is introduced using aviral expression system (such as vaccinia or other pox virus,retrovirus, or adenovirus), which can involve the use of anon-pathogenic (defective), replication competent virus. Suitablesystems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl.Acad. Sci., USA 86:317-21, 1989; Flexner et al., Ann. N.Y. Acad. Sci.569:86-103, 1989; Flexner et al., Vaccine 8:17-21, 1990; U.S. Pat. Nos.4,603,112, 4,777,127, 4,769,330, and 5,017,487; PCT publications WO89/01973 and WO 91/02805; Berkner, Biotechniques 6:616-27, 1988;Rosenfeld et al., Science 252:431-4, 1991; Kolls et al., Proc. Natl.Acad. Sci. USA 91:215-9, 1994; Kass-Eisler et al., Proc. Natl. Acad.Sci. USA 90:11498-502, 1993; Guzman et al., Circulation 88:2838-48,1993; and Guzman et al., Cir. Res. 73:1202-7, 1993. Techniques forincorporating DNA into such expression systems are known. DNA can alsobe incorporated as “naked DNA,” as described, for example, in Ulmer etal., Science 259:1745-9, 1993 and Cohen, Science 259:1691-2, 1993.Uptake of naked DNA can be increased by coating the DNA ontobiodegradable beads.

While any suitable carrier known to those of ordinary skill in the artcan be employed in the pharmaceutical compositions, the type of carrierwill vary depending on the mode of administration. Pharmaceuticalcompositions can be formulated for any appropriate manner ofadministration, including for example, oral (including buccal orsublingual), nasal, rectal, aerosol, topical, intravenous,intraperitoneal, intradermal, intraocular, subcutaneous or intramuscularadministration. For parenteral administration, such as subcutaneousinjection, exemplary carriers include water, saline, alcohol, fat, wax,buffer, or combinations thereof. For oral administration, any of theabove carriers or a solid carrier can be employed. Biodegradablemicrospheres (such as polylactate polyglycolate) can also be employed ascarriers for the pharmaceutical compositions. Suitable biodegradablemicrospheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268 and5,075,109.

The disclosed pharmaceutical compositions can also include buffers (suchas neutral buffered saline or phosphate buffered saline), carbohydrates(such as glucose, mannose, sucrose or dextrans), mannitol, andadditional proteins, polypeptides or amino acids such as glycine,antioxidants, chelating agents such as EDTA or glutathione, andimmunostimulants (such as adjuvants, for example, aluminum phosphate) orpreservatives.

The compositions of the present disclosure can be formulated as alyophilizate, or stored at temperatures from about 4° C. to −100° C.Compositions can also be encapsulated within liposomes using well knowntechnology. Furthermore, the compositions can be sterilized, forexample, by filtration, radiation, or heat.

Any of a variety of immunostimulants can be employed in thepharmaceutical compositions that include an immunogenically effectiveamount of attenuated deoptimized pathogen. In some examples, animmunostimulatory composition also includes one or more compounds havingadjuvant activity, and can further include a pharmaceutically acceptablecarrier.

Adjuvants are non-specific stimulators of the immune system that canenhance the immune response of the host to the immunogenic composition.Some adjuvants contain a substance designed to protect the antigen fromrapid catabolism, for example, aluminum hydroxide or mineral oil, and astimulator of immune responses, such as lipid A, Bordatella pertussis orMycobacterium tuberculosis derived proteins. Suitable adjuvants arecommercially available as, for example, Merck Adjuvant 65 (Merck andCompany, Inc., Rahway, N.J.), TiterMax Gold (TiterMax, Norcross, Ga.),ISA-720 (Seppic, France) ASO-2 (SmithKlineGlaxo, Rixensart, Belgium);aluminum salts such as aluminum hydroxide (for example, Amphogel, WyethLaboratories, Madison, N.J.) or aluminum phosphate; salts of calcium,iron or zinc; an insoluble suspension of acylated tyrosine; acylatedsugars; cationically or anionically derivatized polysaccharides;polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A andsaponins such as quil A and QS-21 (Antigenics, Framingham, Mass.).Cytokines, such as GM-CSF or interleukin-2, -7, or -12, can be used asadjuvants.

The adjuvant composition can be designed to induce an immune responsepredominantly of the Th1 type. High levels of Th1-type cytokines (suchas IFN-γ, TNF-α, IL-2 and IL-12) tend to favor the induction of cellmediated immune responses to an administered antigen. In contrast, highlevels of Th2-type cytokines (such as IL-4, IL-5, IL-6 and IL-10) tendto favor the induction of humoral immune responses. Followingadministration of a pharmaceutical composition as provided herein, asubject may support an immune response that includes Th1- and Th2-typeresponses. However, in examples where the response is predominantly aTh1-type, the level of Th1-type cytokines increases to a greater extentthan the level of Th2-type cytokines. The levels of these cytokines canbe readily assessed using standard assays.

Adjuvants for use in eliciting a predominantly Th1-type responseinclude, but are not limited to, a combination of monophosphoryl lipidA, such as 3-de-O-acylated monophosphoryl lipid A (3D-MPL) (Corixa,Hamilton Ind.), together with an aluminum salt. MPL adjuvants areavailable from Corixa (Seattle, Wash.; see also U.S. Pat. Nos.4,436,727; 4,877,611; 4,866,034 and 4,912,094). CG-containingoligonucleotides (in which the CG dinucleotide is unmethylated) alsoinduce a predominantly Th1 response. Such oligonucleotides are wellknown and are described, for example, in PCT publications WO 96/02555and WO 99/33488. Immunostimulatory DNA sequences are also described, forexample, by Sato et al., Science 273:352, 1996. Another adjuvant is asaponin such as QS21 (Antigenics, Framingham, Mass.), which may be usedalone or in combination with other adjuvants. For example, an enhancedsystem involves the combination of a monophosphoryl lipid A and saponinderivative, such as the combination of QS21 and 3D-MPL as described inWO 94/00153, or a less reactogenic composition where the QS21 isquenched with cholesterol, as described in WO 96/33739. Otherformulations include an oil-in-water emulsion and tocopherol. Anadjuvant formulation involving QS21, 3D-MPL and tocopherol in anoil-in-water emulsion is described in WO 95/17210.

Still further adjuvants include Montanide ISA 720 (Seppic, France), SAF(Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the ASO-2series of adjuvants (SmithKlineGlaxo, Rixensart, Belgium), Detox(Corixa, Seattle, Wash.), RC-529 (Corixa, Seattle, Wash.), Aminoalkylglucosaminide 4-phosphates (AGPs), copolymer adjuvants, CGoligonucleotide motifs and combinations of CG oligonucleotide motifs,bacterial extracts (such as mycobacterial extracts), detoxifiedendotoxins, and membrane lipids. Combinations of two or more adjuvantscan also be used.

Still other adjuvants include polymers and co-polymers. For example,copolymers such as polyoxyethylene-polyoxypropylene copolymers and blockco-polymers can be used. A particular example of a polymeric adjuvant ispolymer P1005.

Adjuvants are utilized in an adjuvant amount, which can vary with theadjuvant, subject, and immunogen. Typical amounts of non-emulsionadjuvants can vary from about 1 ng to about 500 mg per administration,for example, from 10 μg to 800 μg, such as from 50 μg to 500 μg. Foremulsion adjuvants (oil-in-water and water-in-oil emulsions) the amountof the oil phase can vary from about 0.1% to about 70%, for examplebetween about 0.5% and 5% oil in an oil-in-water emulsion and betweenabout 30% and 70% oil in a water-in-oil emulsion. Those skilled in theart will appreciate appropriate concentrations of adjuvants, and suchamounts can be readily determined.

Any pharmaceutical composition provided herein can be prepared usingwell known methods that result in a combination of deoptimized pathogen(or deoptimized DNA coding sequence), alone or in the presence of animmunostimulant, carrier or excipient, or combinations thereof. Suchcompositions can be administered as part of a sustained releaseformulation (such as a capsule, sponge or gel that includes thedeoptimized pathogen) that provides a slow release of the compositionfollowing administration. Such formulations can be prepared using wellknown technology (see, for example, Coombes et al., Vaccine 14:1429-38,1996) and administered by, for example, subcutaneous implantation at thedesired target site. Sustained-release formulations can contain adeoptimized pathogen dispersed in a carrier matrix or contained within areservoir surrounded by a rate controlling membrane.

Carriers for use with the disclosed compositions are biocompatible, andcan also be biodegradable, and the formulation can provide a relativelyconstant level of active component release. Suitable carriers include,but are not limited to, microparticles of poly(lactide-co-glycolide), aswell as polyacrylate, latex, starch, cellulose and dextran. Otherdelayed-release carriers include supramolecular biovectors, whichcomprise a non-liquid hydrophilic core (such as a cross-linkedpolysaccharide or oligosaccharide) and, optionally, an external layercomprising an amphiphilic compound, such as a phospholipid (see, forexample, U.S. Pat. No. 5,151,254 and PCT publications WO 94/20078,WO/94/23701 and WO 96/06638). The amount of active compound containedwithin a sustained release formulation depends upon the site ofimplantation, the rate and expected duration of release and the natureof the condition to be treated or prevented.

Any of a variety of delivery vehicles can be employed with the disclosedpharmaceutical compositions to facilitate production of anantigen-specific immune response to a deoptimized pathogen. Exemplaryvehicles include, but are not limited to, hydrophilic compounds having acapacity to disperse the deoptimized pathogen and any additives. Thedeoptimized pathogen can be combined with the vehicle according tomethods known in the art. The vehicle can be a solvent or dispersionmedium containing, for example, water, ethanol, polyol (for example,glycerol, propylene glycol, liquid polyethylene glycol, and the like),and suitable mixtures thereof. Other exemplary vehicles include, but arenot limited to, copolymers of polycarboxylic acids or salts thereof,carboxylic anhydrides (for example, maleic anhydride) with othermonomers (for example, methyl (meth)acrylate, acrylic acid and thelike), hydrophilic vinyl polymers, such as polyvinyl acetate, polyvinylalcohol, polyvinylpyrrolidone, cellulose derivatives, such ashydroxymethylcellulose, hydroxypropylcellulose and the like, and naturalpolymers, such as chitosan, collagen, sodium alginate, gelatin,hyaluronic acid, and nontoxic metal salts thereof.

A biodegradable polymer can be used as a base or vehicle, such aspolyglycolic acids and polylactic acids, poly(lactic acid-glycolic acid)copolymer, polyhydroxybutyric acid, poly(hydroxybutyric acid-glycolicacid) copolymer, and mixtures thereof. Other biodegradable orbioerodable polymers include, but are not limited to, such polymers aspoly(epsilon-caprolactone), poly(epsilon-aprolactone-CO-lactic acid),poly(epsilon.-aprolactone-CO-glycolic acid), poly(beta-hydroxy butyricacid), poly(alkyl-2-cyanoacrilate), hydrogels, such as poly(hydroxyethylmethacrylate), polyamides, poly(amino acids) (for example, L-leucine,glutamic acid, L-aspartic acid and the like), poly(ester urea),poly(2-hydroxyethyl DL-aspartamide), polyacetal polymers,polyorthoesters, polycarbonate, polymaleamides, polysaccharides, andcopolymers thereof. In some examples, vehicles include synthetic fattyacid esters such as polyglycerin fatty acid esters and sucrose fattyacid esters. Hydrophilic polymers and other vehicles can be used aloneor in combination, and enhanced structural integrity can be imparted tothe vehicle by partial crystallization, ionic bonding, cross-linking andthe like.

The vehicle can be provided in a variety of forms, including, fluid orviscous solutions, gels, pastes, powders, microspheres and films. In oneexample, pharmaceutical compositions for administering a deoptimizedpathogen are formulated as a solution, microemulsion, or other orderedstructure suitable for high concentration of active ingredients. Properfluidity for solutions can be maintained, for example, by the use of acoating such as lecithin, by the maintenance of a desired particle sizein the case of dispersible formulations, and by the use of surfactants.

Delivery vehicles include antigen presenting cells (APCs), such asdendritic cells, macrophages, B cells, monocytes and other cells thatcan be engineered to be efficient APCs. Such cells can, but need not, begenetically modified to increase the capacity for presenting theantigen, to improve activation or maintenance of the T cell response, tohave anti-pathogen effects, or to be immunologically compatible with thereceiver (matched HLA haplotype). APCs can generally be isolated fromany of a variety of biological fluids and organs, including tumor andperitumoral tissues, and may be autologous, allogeneic, syngeneic orxenogeneic cells.

In certain examples, the deoptimized pathogen is administered in a timerelease formulation. These compositions can be prepared with vehiclesthat protect against rapid release, and are metabolized slowly underphysiological conditions following their delivery (for example in thepresence of bodily fluids). Examples include, but are not limited to, apolymer, controlled-release microcapsules, and bioadhesive gels. Manymethods for preparing such formulations are well known to those skilledin the art (see, for example, Sustained and Controlled Release DrugDelivery Systems, J. R. Robinson, ed., Marcel Dekker, Inc., New York,1978).

Pharmaceutical compositions can be presented in unit-dose or multi-dosecontainers, such as sealed ampoules or vials. Such containers aretypically hermetically sealed to preserve sterility of the formulationuntil use. In general, formulations can be stored as suspensions,solutions or as emulsions in oily or aqueous vehicles. Alternatively, apharmaceutical composition can be stored in a freeze-dried conditionrequiring only the addition of a sterile liquid carrier immediatelyprior to use.

The pharmaceutical compositions of the disclosure typically are sterileand stable under conditions of manufacture, storage and use. Sterilesolutions can be prepared by incorporating the disclosed deoptimizedpathogens (alone or in the presence of a pharmaceutically acceptablecarrier, adjuvant, or other biologically active agent) in the desiredamount in an appropriate solvent followed by sterilization, such as byfiltration. Generally, dispersions are prepared by incorporating thedeoptimized pathogen into a sterile vehicle that contains a dispersionmedium and other desired ingredients. In the case of sterile powders,methods of preparation include vacuum drying and freeze-drying whichyields a powder of the deoptimized pathogen plus any additional desiredingredient from a previously sterile-filtered solution thereof. Forvaccine use, the deoptimized pathogens of the disclosure can be useddirectly in vaccine formulations, or lyophilized, as desired, usinglyophilization protocols well known in the art. Lyophilized pathogen istypically be maintained at about 4° C. When ready for use thelyophilized pathogen can be reconstituted in a stabilizing solution(such as saline).

Example 24 Methods of Stimulating an Immune Response

This example describes methods using the disclosed immunogeniccompositions that can be used to stimulate an immune response in asubject, such as a human. Methods for inoculation are routine in theart. In some examples, a determination is made as to whether the subjectwould benefit from administration of a deoptimized pathogen sequence,prior to administering the immunogenic composition. Administration canbe achieved by any method known in the art, such as oral administrationor inoculation (such as intramuscular, ip, or subcutaneous). In someexamples, the deoptimized pathogen is administered, for example aninactivated or live pathogen. In particular examples, the deoptimizednucleic acid molecule or protein molecule is administered. In someexamples, combinations of these agents are administered, alone or in thepresence of other agents, such as an adjuvant.

The amount of deoptimized pathogen (or part thereof such as DNAsequence) administered is sufficient to induce in the host an effectiveimmune response against virulent forms of the pathogen. An effectiveamount can being readily determined by one skilled in the art, forexample using routine trials establishing dose response curves. Theimmunogenic compositions disclosed herein can be administered to thesubject as needed to confer immunity against the pathogen to thesubject. For example, the composition can be administered in a singlebolus delivery (which can be followed by one or more boosteradministrations as needed), via continuous delivery over an extendedtime period, in a repeated administration protocol (for example, by anhourly, daily, weekly, or monthly repeated administration protocol).

In some examples, a deoptimized viral sequence is administered to asubject. The sequence can be administered as a nucleic acid molecule,the virus itself, or combinations thereof. In one example, a deoptimizedDNA sequence is administered to the subject, for example in the presenceof a carrier molecule, such as a lipid (for example a liposome). Theamount of DNA administered can be determined by routine methods in theart. In some examples, the amount of DNA administered (for example byorally or inoculation) is 0.1 μg-1000 μg DNA, such as 10-100 μg DNA,such as at least 10 μg DNA. In particular examples, a deoptimized virus(live or inactivated, and in some examples lyophilized) is administeredto the subject (for example orally or via injection). Exemplary doses ofvirus, include, but are not limited to, 10³ to 10¹⁰ plaque forming units(PFU) or more of virus per dose, such as 10⁴ to 10⁵ PFU virus per dose,for example at least 10³ PFU virus per dose, at least 10⁴ PFU virus perdose, at least 10⁵ PFU virus per dose, or at least 10⁹ PFU virus perdose.

In some examples, a deoptimized bacterial sequence is administered to asubject. The sequence can be administered as a nucleic acid molecule, oras the bacterium. In examples wherein a deoptimized bacterial DNAsequence is administered, the methods described above can be used. Inparticular examples, a deoptimized bacterium (such as an inactivatedwhole-cell vaccine) is administered to the subject (for example orallyor via injection). Exemplary doses of bacteria (as measured bycolony-forming units), include, but are not limited to, 10³-10¹⁰bacteria per dose, for example at least 10³ bacteria, at least 10⁴bacteria, at least 10⁵ bacteria, at least 10⁸ bacteria, or at least 10⁹bacteria per dose.

In some examples, a deoptimized parasitic sequence is administered to asubject. The sequence can be administered as a nucleic acid molecule, oras the parasite. In examples wherein a deoptimized parasitic DNAsequence is administered, the methods described above can be used. Inparticular examples, a deoptimized parasite (such as a live orinactivated parasite) is administered to the subject (for example orallyor via injection). Exemplary doses of parasites, include, but are notlimited to, 10³-10¹⁰ parasites per dose, for example at least 10³parasites, at least 10⁴ bacteria, at least 10⁵ parasites, at least 10⁸parasites, or at least 10⁹ parasites per dose.

Example 25 Attenuated Poliovirus as an Immunogen

This example describes methods that can be used to demonstrate theability of an attenuated poliovirus to be used as an immunogen.

Wild-type mouse neurovirulence using deoptimized MEF1 viruses

The method of Ford et al. (Microbial Pathogenesis 33:97-107, 2002,herein incorporated by reference) can be used. Wild-type mice areinfected with the wild type 2 poliovirus strain MEF1. MEF1 is amouse-adapted type 2 polio strain that cannot infect mice via the oralroute, but can infect via injection. Briefly, wild-type mice (such assix-week old, adult, male Swiss mice (Taconic Labs, Germantown, N.Y.))are anesthetized with isofluorane and subsequently administered thevirus via intramuscular injection (right medial gastrocnoemius)utilizing a 26.5 gauge needle. In some examples, the virus is injectedinto the brain or spinal cord. Mice each are administered approximately10¹⁰-10¹¹ TCID50 (amount of virus required for 50% infectivity ofsusceptible cells in tissue culture) of MEF1R2 (an MEF1 clone with anextra silent restriction site; SEQ ID NO: 53), MEF1 (non-clone; SEQ IDNO: 52), MEF1R5 (VP1 alterations; SEQ ID NO: 54), MEF1R9 (SEQ ID NO:58), or with phospho-buffered saline (PBS) as a negative control.

All inoculated animals are observed daily for signs of disease(paralysis, encephalitis, or death). Paralysis is defined as limbweakness and delineated between spastic/hypertonic and flaccid/hypotonicby a neurologist. Tone is determined by manual manipulation of the limband compared with normal tone in uninoculated mice. Blood will becollected from mice 21 days after infection. Serum samples are analyzedfor the presence of neutralizing antibody to poliovirus. Blood will becollected before euthanasia when necessary.

The following methods can be used to assess immunogenicity of thedeoptimized viruses. The presence of neutralizing antibodies can beassessed by using the neutralization test (standard WHO method), asdescribed in Horie et al. (Appl. Environ. Microbiol. 68:138-42, 2002).Following immunization, sera is obtained from immunized andnon-immunized subjects. About 50 μl of sera dilution series is prepared,in duplicate, in Eagle's minimal essential medium (MEM) supplementedwith 2% FCS in a 96-well microtiter plate. Then 50 μl of 100 50% cellculture infectious doses (CCID50) of each isolate, Sabin type 2 vaccinestrain, or type 2 wild strain MEF1 is added to each well. Afterincubation at 36° C. for 2 hours, 100 μl of a cell suspension containing10⁴ HEp2-C cells in MEM supplemented with 5% FCS are added to each well.The plates are then scored or CPE after 7 days of incubation at 36° C.in a CO₂ atmosphere. The calculation of the neutralizing titer of eachsample can be determined by the Karber method (see World HealthOrganization. 1990. Manual for the virological investigation ofpoliomyelitis. World Health Organization, Expanded Programme onImmunization and Division of Communicable Diseases. W.H.O. publicationno. W.H.O./EPI/CDS/POLIO/90.1. World Health Organization, Geneva,Switzerland).

Production of specific neutralizing antibodies when inoculated withcodon-deoptimized virus constructs of MEF1 would give evidence ofprotective immunity Protection from paralysis upon challenge withdosages of MEF1 sufficient to cause paralysis in unprotected mice wouldbe confirmation of protective immunity.

Transgenic Mice Bearing the Human Poliovirus Receptor

As an alternative to using wild-type mice, transgenic mice expressingthe human poliovirus receptor can be used (PVR-Tg21 mice, CentralLaboratories for Experimental Animals, Kanagawa, Japan), using themethods described above. Briefly, transgenic PVR-Tg21 mice at 8-10 weeksof age are administered the deoptimized virus (such as a sequence thatincludes SEQ ID NO: 5 or 58), wild-type virus, other polio virus, orbuffer alone. Administration can be by any mode, such as injection intothe muscle as described above, intranasal, intraspinal or intracerebralinoculation. However, injection into muscle in some examples requires ahigher dose of virus than intraspinal or intracerebral inoculation.Intraspinal injection can be performed as described in Horie et al.(Appl. Envir. Microbiology 68:138-142, 2002). Briefly, the desired virusis serially diluted 10-fold, and 5 μl of each dilution inoculated intothe spinal cord of 5-10 mice per dilution. Intracerebral injection canbe performed as described in Kew et al. (Science 296:356-9, 2002).Briefly, mice are inoculated (30 μl/mouse) intracerebrally for eachvirus dilution (in 10-fold increments). Intranasal infection can beperformed using the method of Nagata et al. (Virology 321:87-100, 2004),as transgenic mice are susceptible to polio infection via the intranasalroute.

Analysis of Challenge/Protection

After the neurovirulence properties of the codon-deoptimized viruses aredetermined, challenge studies can be used to demonstrate that thecodon-deoptimized viruses protect mice from disease. Briefly, mice areinoculated with a codon-deoptimized virus using conditions that induceneutralizing antibody Immunized mice are challenged 21 days later withneurovirulent type 2 MEF1 virus at paralytic doses. The absence ofparalytic signs when challenged with neurovirulent prototype MEF1indicates that the transgenic PVR-Tg21 mice are protected by their priorexposure to codon-deoptimized MEF1 virus. The type-specificity ofprotection is measured by challenge with the neurovirulent type 1poliovirus, Mahoney and neurovirulent type 3 poliovirus.

Monkey Neurovirulence

As an alternative to using mice, the ability of a deoptimized poliovirusto be used as an immunogen can be determined in rhesus monkeys.Deoptimized polioviruses, such as those disclosed herein, can beadministered to monkeys and neurovirulence assayed. Examples ofdeoptimized viruses include, but are not limited to sequences thatinclude SEQ ID NOS: 5, 8, 58, or 65-70). Briefly, intraspinalinoculation of rhesus monkeys will be performed according to therecommendations of the World Health Organization for Type 2 OPV (WHOTech. Rep. Ser. 800, 30-65, 1990). Requirements for poliomyelitisvaccine (oral), and the United States Code of Federal Regulations, Title21, Part 630.16 (1994). For example, 10-14 juvenile rhesus monkeys willbe inoculated in the lumbar region of the spinal cord with 0.1-0.2 ml ofvirus (6-7 log₁₀ CCID₅₀/monkey). The ability of the deoptimized virus tostimulate an immune response in the treated monkeys can be determined asdescribed above.

Example 26 Methods of Determining Replicative Fitness

This example describes methods that can be used to measure thereplicative fitness of a virus or bacteria. One skilled in the art willappreciate that other methods can also be used.

In one example, the replicative fitness of a deoptimized virus isdetermined by calculation of plaque size and number. Briefly, RNAtranscripts of viral sequences having a deoptimized sequence or a nativesequence are transfected into the appropriate cell line. The resultingvirus obtained from the primary transfection can be passaged again toincrease virus titers. The virus is then used to infect cells (such asconfluent HeLa cell monolayers), and incubated at room temperature for10-60 minutes, such as 30 minutes, prior to the addition of 0.45% SeaKemLE Agarose (BioWhittaker Molecular, Rockland, Me.) in culture medium.Plates are incubated for 50-100 hours at 35° C. (or at a temperaturemost appropriate for the virus strain under study), fixed with 0.4%formaldehyde and stained with 3% crystal violet. Plaque size is thequantified, for example by manual measurement and counting of theplaques, or by scanning plates (for example on a FOTO/Analyst Archiversystem, Fotodyne, Hartland, Wis.) and subsequent image analysis (forexample using Scion Image for Windows, Scion Corp., Frederick, Md.). Acodon-deoptimized virus is considered to have reduced replicativefitness when the size or number of plaques is reduced by at least 50%,for example at least 75%, as compared to the size or number of plaquesgenerated by the native virus.

The replicative fitness of a virus can also be determined usingsingle-step growth experiments. Virus (deoptimized and native) isgenerated as described above. The appropriate cells (such as HeLa cells)are infected at a multiplicity of infection (MOI) of 1-10 PFU/cell withstirring for 10-60 minutes at 35° C. Cells are then sedimented bylow-speed centrifugation and resuspended in culture media. Incubationcontinued at 35° C. in a water bath with orbital shaking at 300 rpm.Samples are withdrawn at 2-hour intervals from 0 to 14 hourspostinfection, and titered by plaque assay as described above.

To determine the replicative fitness of a bacterium or yeast pathogen, acolony-forming assay can be performed. Briefly, bacterial or yeastsuspensions can be plated onto agar plates containing solidified mediumwith the appropriate nutrients, and after incubation (normally at 37°C.), the number of colonies are counted. Alternatively, growth rates canbe measured spectrophotometrically by following the increase in opticaldensity of the appropriate liquid medium after inoculation with thebacterial or yeast cultures. Another method to measure growth rateswould use quantitative PCR to determine the rate of increase of specificnucleic acid targets as the bacterial or yeast cells are incubated inthe appropriate liquid medium.

In view of the many possible embodiments to which the principles of ourinvention may be applied, it should be recognized that the illustratedexamples are only particular examples of the invention and should not betaken as a limitation on the scope of the invention. Rather, the scopeof the invention is defined by the following claims. We therefore claimas our invention all that comes within the scope and spirit of theseclaims.

We claim:
 1. A method of attenuating a bacterium, comprising preparing abacterial nucleic acid molecule comprising at least twenty deoptimizedcodons in a coding sequence of the bacterium by replacing each of the atleast twenty codons in the coding sequence with a synonymous codon lessfrequently used in the bacterium, thereby generating an attenuatedbacterium comprising a deoptimized bacterial nucleic acid molecule. 2.The method of claim 1, wherein the bacterial nucleic acid moleculecomprises replacement of at least 50-2000 codons with synonymous codonsless frequently used in the bacterium.
 3. The method of claim 1, whereinreplicative fitness of the attenuated bacterium is reduced by at least20% as compared to an amount of replicative fitness by the bacteriumhaving a coding sequence with a native codon composition.
 4. The methodof claim 1, wherein replicative fitness of the attenuated bacterium isreduced by 10-98% as compared to replicative fitness of the bacteriumwith a native codon composition.
 5. The method of claim 1, wherein thedeoptimized bacterial nucleic acid molecule comprises replacement of atleast 50% of the coding sequence with synonymous codons less frequentlyused in the bacterium.
 6. The method of claim 1, wherein the deoptimizedbacterial nucleic acid molecule alters the number of CG dinucleotides,the number of TA dinucleotides, or the number of CG dinucleotides and TAnucleotides in the coding sequence by at least 20%.
 7. The method ofclaim 6, wherein the deoptimized bacterial nucleic acid moleculeincreases the number of CG dinucleotides or TA dinucleotides in thecoding sequence by at least 100%.
 8. The method of claim 1, wherein thedeoptimized bacterial nucleic acid molecule comprises a coding sequencehaving an increased number of CG dinucleotides, TA dinucleotides, or CGdinucleotides and TA nucleotides in the coding sequence, wherein the CGor TA dinucleotides fall across codon boundaries.
 9. The method of claim1, wherein the deoptimized bacterial nucleic acid molecule is introducedinto the bacterial genome.
 10. The method of claim 1, wherein thebacterium is a gram-negative bacterium.
 11. The method of claim 10,wherein the gram-negative bacterium is Escherichia coli, Shigelladysenteriae, or Vibrio cholerae.
 12. The method of claim 11, wherein thebacterium is E. coli and wherein at least 20 codons in an ArgS or TufAcoding sequence are deoptimized or the bacterium is Shigella dysenteriaeand at least 20 codons in a RdsB coding sequence are deoptimized. 13.The method of claim 12, wherein the deoptimized coding sequencecomprises a sequence having at least 90% sequence identity to SEQ ID NO:48 or SEQ ID NO:
 51. 14. The method of claim 13, wherein the deoptimizedcoding sequence comprises a sequence shown in SEQ ID NO: 48 or SEQ IDNO:
 51. 15. The method of claim 1, wherein the bacterium is agram-positive bacterium.
 16. The method of claim 15, wherein thegram-positive bacterium is Bacillus anthracis, Staphylococcus aureus,pneumococcus, gonococcus, or streptococcal meningitis.
 17. The method ofclaim 16, wherein the bacterium is Staphylococcus aureus and at leasttwenty codons in an RplB or FusA coding sequence are deoptimized.